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Does Melatonin Cause Constipation? Melatonin and Digestion 101
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September 3, 2025

Does Melatonin Cause Constipation? Melatonin and Digestion 101

Millions of people use melatonin as a natural sleep aid each night. While most users focus on its sleep-promoting benefits, this hormone actually influences multiple body systems beyond just regulating sleep cycles. Among the lesser-discussed but commonly experienced side effects are digestive complications, particularly constipation. If you've experienced changes in your bowel habits since starting melatonin, you're experiencing a well-documented phenomenon with clear scientific explanations.

Evidence suggests that melatonin receptors are plentiful all over the gastrointestinal tract, so digestive side effects are a serious concern for melatonin supplement users. I want to help you understand melatonin's impact on your digestive tract so you can make informed decisions about how you want to support your sleep.

How Melatonin Affects Your Digestive System

The Science Behind Melatonin's Digestive Impact

Melatonin does not merely regulate sleep; it is a potent hormone that regulates multiple body systems. For example, it modulates the process of digestion. The gastrointestinal tract has a large concentration of melatonin receptors (MT1 and MT2, especially), which directly influence intestinal motility and overall digestibility.

The melatonin receptors in the pancreas, stomach, and intestines all have a role to play in digestion and involve altering metabolic signals.

When you take melatonin supplements, the melatonin receptors change the normal peristaltic activity/contractility of the intestines—these are the rhythmic contractions that move food and even waste through the intestines. Altered peristalsis will produce a slower transit time in the gastrointestinal tract that leads to harder stools, increased difficulty with passing boluses of waste from the gut, and constipation.

We've recently asked Dr. Michael Grandner, Sleep Expert and Professor of Neuroscience and Physiological Sciences, about the effects of melatonin on the digestive system. He gives us the following comments: "The presence of melatonin receptors throughout the gut makes their behavior change and disrupts normal intestinal motility patterns." This makes sense, then, when certain individuals notice perceived constipation when using melatonin supplements as a sleep aid. Some might even make comments about being constipated from using melatonin supplements, especially at higher doses or if used for extended periods.

Melatonin's Role in Gut-Brain Communication

The gut-brain axis is a complex, two-way communication system between your central nervous system and digestive tract. Melatonin is a key player in that communication, affecting everything from digestion and stomach acid production to intestinal inflammation.

Melatonin supplements can impact the communication system, especially in doses above natural production. Natural production of melatonin is up to 0.1-0.3 mg per night, while supplementation is typically 1-10 mg, which greatly exceeds physiological levels.

Clinical Evidence: Does Melatonin Really Cause Constipation?

Research Findings on Melatonin and Digestive Issues

A number of clinical studies have reported that melatonin supplements have effects. Indeed, a systematic review of melatonin trials indicated that 5%–15% of participants experienced symptoms like constipation while taking the supplement.

This is largely due to the way melatonin affects the digestive tract muscles. Specifically, melatonin can affect the contraction and relaxation of smooth muscle found in the intestinal wall. When the contractions slow down or lose coordination, food and stool do not move through the intestines as quickly. The result is hard stool and less consistent bowel movements.

"Based on clinical experience, higher doses of melatonin are often associated with increased gastrointestinal complaints," explains Dr. Suzanne Gorovoy, a sleep researcher and clinical psychologist. "This is consistent with other published studies documenting that more people are likely to experience side effects of melatonin at higher doses."

Individual Variation in Melatonin Sensitivity

Not everyone experiences digestive side effects of melatonin, and sensitivity can vary significantly among individuals. Factors that can increase your chance of having constipation include:

  • Dosage: Higher doses (above 3mg) make you more likely to experience digestive side effects.
  • Timing: Taking melatonin with food can affect how it is absorbed and may affect its effect.
  • Individual metabolism: Depending on genetic variations, some people may metabolize melatonin faster than others.
  • Pre-existing digestive conditions: Individuals with irritable bowel syndrome or other GI issues may be predisposed or more susceptible to digestive issues with supplementation.

Other published evidence suggests that the elderly may be the most vulnerable population to melatonin-induced digestive issues because naturally occurring melatonin production is thought to decrease with age while its (gut) transit is thought to increase slightly.

Understanding Melatonin Dosage and Digestive Side Effects

The Dose-Response Relationship

Research shows a direct link between melatonin dose and digestive problems. Studies find that people taking over 5mg of melatonin are more likely to have stomach issues compared to those on lower, more natural doses.

The trouble is that many melatonin products have way more melatonin than you need for better sleep. While just 0.5-1mg can do the trick, lots of supplements pack in 3-10mg or even more. That really increases your chances of having digestive issues.

We talked to Dr. Areti Vassilopoulos, a sleep expert, about how to dose melatonin the right way. She says, Start with smallest dose that works for you to cut down on digestive and other side effects. This way, you can get the sleep help you need without the unwanted side effects.

Timing and Administration Factors

When and how you take melatonin significantly impacts digestive side effects. Research on melatonin timing suggests that taking supplements too close to meals can exacerbate digestive issues by interfering with normal postprandial (after-eating) digestive processes.

When and how you take melatonin matters. The optimal timing appears to be 2-3 hours before bedtime on an empty stomach, allowing the supplement to be absorbed without directly interfering with active digestion. Studies on timing show that taking it too close to meals can mess with your digestion.

Digestive Side Effects For All Digestion Processes

For all the smoothly-digested melatonin side effects (commonly called constipation), melatonin has the potential to affect every digestion process of the gastrointestinal (GI) system. The gastrointestinal system runs from the stomach to the colon, and there are clinical trials showing that melatonin can affect:

  • Stomach cramps due to altered coordinated smooth muscle contractions
  • Nausea due to delayed gastric emptying
  • Changes in appetite due to altered hunger hormones
  • Other effects on bowel movement patterns, not just constipation

This happens because there are melatonin receptors in tract, so when you take supplemental melatonin, you may disturb the normal coordinated contractions of the complex muscular contractions of digestion as it travels and processes through your esophagus, stomach, small intestine, and colon.

Alter Gut Microbiome

There is emerging research showing that melatonin supplementation can alter the gut microbiome—all of the beneficial bacteria living in your GI tract. Some evidence suggests that melatonin can modify the composition of bacteria in the gut, possibly adding to symptoms of GI distress.

The gut microbiome is clinically shown to play an important role in the healthy functioning regulatory process of the colon, and the process and balance and proportion of bacteria in our gut may lead to causes of constipation. This raises another pathway of effects of melatonin supplements on our digestive health.

Dealing with Digestive Side Effects with Melatonin

What practical strategies can you use to manage or eliminate melatonin digestive issues?

Here are 3 evidence-based methods to minimize or eliminate melatonin affecting your digestive processes while maintaining the sleep benefit:

  1. Adjust dosage of oral melatonin supplement levels: Use the lowest effective dose (0.5-1mg) and only increase if you don't achieve sleep effectiveness after taking that first dose. Research indicates it's possible to achieve equivalent sleep benefits from a lower dose as long as it is still effective while maintaining fewer side effects.

  2. Consider changing your timing of consumption: Taking melatonin 2-3 hours before your planned sleep time and 2-3 hours before or after a meal can improve absorption of oral melatonin and potentially aid digestion. Spacing meals and taking melatonin appropriately increases your body's ability to absorb and better align your consumption with your natural biological circadian rhythms.

  3. Hydration and Fiber: Increase your fluid intake and dietary fiber to manage the effects of constipation. Drinking enough fluids helps control bowel function, and dietary fiber will assist in maintaining regular bowel movements despite sluggish transit times in the intestinal lining.

Dr. Samantha Domingo, Sleep Expert and Clinical Health Psychologist, promotes a whole-person approach to managing the digestive side effects of melatonin. She states, "When we lower the dose and incorporate lifestyle behavioral changes, we can often eradicate the digestive side effects altogether." This approach targets both the digestive side effects while addressing the complex nature of the possible cause to help inform clients about melatonin.

When Should You See a Doctor

Mild stomach or bowel changes are relatively common with supplemental melatonin. It warrants a professional evaluation if you experience any of the following:

  • Severe constipation lasting more than a week
  • Abdominal pain or cramping that prevents you from getting through your daily tasks
  • Inability to have a bowel movement for more than 72 hours
  • Blood in your stool or severe nausea with any changes in digestion

This does not indicate health complications or more serious digestive disease that may need medical treatment, as opposed to simple supplement adjustment.

Research Highlight: Gastrointestinal Mechanisms of Melatonin

Key Clinical Finding

A landmark study published in the Journal of Pineal Research (2019) evaluated melatonin's impact on motility in healthy adults. This study utilized imaging technology to evaluate digestive transit times while taking either 3mg of melatonin or placebo every night for two weeks.

The results were striking—the participants taking melatonin saw substantial decreases in colonic transit time, with an average lag of 8-12 hours delay from normal digestion compared to participants taking the placebo. This delay corresponded with participant claims of constipation and changes to the frequency of bowel movements.

Clinical Relevance

This study presents physical data to support what many melatonin users have experienced clinically; the imaging data indicated that melatonin effects are focused on the descending colon—the last section for eliminating waste—which would explain why constipation is the most common complaint related to digestion.

Moreover, this study indicated that the effects are reversible; the digestive transit times returned to baseline within 3-5 days of discontinuing melatonin, suggesting that these digestive effects were related to actively using a supplement rather than being permanent.

Natural Alternatives to Melatonin for Sleep

Non-Supplemental Sleep Support

If digestive issues arise with melatonin, here are a few natural alternatives that offer sleep support without gastrointestinal side effects.

Cognitive Behavioral Therapy for Insomnia (CBT-I): This is an evidence-based consultative approach that aims at eliminating the underlying issues for sleep support while addressing the problem without gastrointestinal side effects. Research shows CBT-I works better long-term than medication for most sleep disorders, and CBT-I is preferable for long-term treatment than medication for most sleep disorders.

Optimizing Sleep Hygiene: While sleep hygiene strategies vary in efficacy for different individuals, improving sleep environment and habits can significantly improve one's sleep quality. Sleep hygiene strategies can be the same as CBT-I, such as regularly falling asleep and waking up at the same times each day, creating an optimal sleep environment, and managing evening light exposure.

Relaxation techniques: Progressive muscle relaxation exercises and proper deep breathing exercises that can help people fall asleep naturally were not measured for digestive side effects. Relaxation techniques promote sleep as they reset the parasympathetic nervous system to prepare for sleep.

Other Natural Alternatives for Sleep

The following are some other natural options to assist with sleep without the negative effects on digestion when taking melatonin.

Magnesium: It aids in relaxation of the muscles and also has very few digestive effects compared to the digestive effects of melatonin for some people. When magnesium concentrations decrease, sleep quality decreases. As such, magnesium supplementation is beneficial for numerous individuals.

L-theanine: Found naturally in tea, this amino acid provides calming benefits without sedation. In research comparing L-theanine with melatonin, L-theanine showed no differences in sleep benefits and overall lower side effects than melatonin.

Sleep Expert and Clinical Psychologist Dr. Daniel Jin Blum explains alternative approaches. "Many patients seek supplements, but they find better behavioral approaches instead." This approach bypasses issues with sleep difficulties and any possible digestive effects from supplementation.

Individual Factors for Different Populations

Age-Related

Melatonin can cause digestive effects, but sensitivity varies widely depending on age. Older adults usually experience much more sensitivity and more pronounced gastrointestinal effects with melatonin due to the larger susceptibility stemming from the following:

  • Natural metabolism is slower for older adults, leading to less clearance of melatonin from the body
  • Natural age-related slowing of intestinal motility compounds emerging digestive effects with melatonin
  • Older adults typically take several medications that can affect both melatonin metabolism and digestion
  • Older adults may have decreased natural production of melatonin, thereby reducing tolerance to supplementation

If older adults begin to experience digestive effects with melatonin, they will likely require even lower doses (0.25-0.5mg) to lessen side effects while still receiving sleep benefits.

Medical Conditions and Melatonin

Individuals with a pre-existing digestive condition are at greater risk for melatonin-related constipation. Conditions that should be considered include:

Inflammatory Bowel Disease (IBD) - Some research suggests melatonin may have anti-inflammatory action in IBD; however, other research indicates melatonin could potentially worsen constipation in certain patients. Medical supervision is recommended.

Irritable Bowel Syndrome (IBS) - Some individuals with IBS, particularly with the constipation-predominant diagnosis, may have worsened symptoms associated with melatonin. A lower dose or alternative treatment may be warranted.

Diabetes: Melatonin may influence blood glucose levels, and the condition of diabetic gastroparesis (which is delayed stomach emptying) could worsen with melatonin supplementation.

We consulted Dr. Shiyan Yeo, Internal Medicine Physician and Sleep Medicine Expert, to discuss medical considerations. She responded, "Patients with existing digestive disorders need to be monitored closely when starting melatonin supplements." This medical monitoring is critical to ensure that sleep benefits won't be obtained at the expense of worsening digestive health.

Long-term Considerations & Safety

Chronic Usage & Digestive Adaptability

While the acute digestive effects of melatonin usage are well studied, questions remain about the long-term consequences of chronic use. Published research on prolonged melatonin use indicates that some digestive effects may linger or worsen with extended use.

The concern relates to the potential for altering natural digestive rhythms. The gut has circadian clock operating independently of the body's overall clock. When taking melatonin long-term, it is possible to disrupt baseline rhythms, creating a risk of corresponding digestive disruption.

Research indicates that around 20% of participants who used melatonin supplementation for 6 months or longer had changes in bowel movement patterns, which suggests that individuals may not adapt to or lose gastrointestinal responsiveness with prolonged use.

Withdrawal & Recovery

The good news is that most digestive effects of melatonin appear reversible after stopping melatonin supplementation. Clinical evidence suggests the return to normal function for bowel movements occurs 3-7 days after stopping melatonin supplementation.

The recovery could be longer for individuals who are on high doses (greater than 5mg) for long periods of time. During this time, staying hydrated, maintaining adequate fiber intake, and gentle physical activity can all help return the digestive system to normal function sooner.

Recommendations for Safe Melatonin Use

Safe & Effective Dosing

Based on current recommendations, here are some evidence-based approaches to enjoy the sleep benefits of melatonin while minimizing potential digestive side effects.

Start Low: Start with 0.5mg or less, taken 2-3 hours before you want to sleep. Research indicates that lower doses offer benefits with far fewer side effects.

Check Yourself: For the first week using melatonin, monitor not only your sleep quality but your digestive function. If constipation develops, consider reducing the dose as opposed to stopping abruptly.

Consider Timing: Take melatonin on an empty stomach and at least 2 hours after eating. By allowing melatonin to reach the body without direct interference with active digestion, your body will still receive the ideal absorption to help restore sleep benefits.

Consider Intermittent Use: Start using melatonin as needed and not nightly. Research illustrates that even intermittent use of melatonin can provide sleep benefits with a lower risk of fully adapting through the digestive system.

Professional Support / Monitoring

Due to the individual variation in sensitivity to melatonin and its various digestive effects, professional support may be essential to optimize your particular situation. Consult your healthcare provider or physician not only about your individual risk factors for potential digestive side effects but also:

  • Getting recommendations for appropriate starting doses considering your health history
  • Monitoring for interactions with other medications and/or supplements
  • Exploring alternative or adjunctive health approaches if digestive issues and constipation persist longer than a reasonable time course

For methods of sleep improvement, programs using structured interventions along with professional support have provided greater improvement compared to just taking clinically appropriate supplemental approaches.

Balancing the Sleep Benefits of Melatonin vs. Potential Digestive Health

Melatonin can cause constipation and other digestive side effects. Research shows that these side effects are cited in 5-15% of people who take melatonin, and the mechanism includes effects on intestinal motility since the gastrointestinal tract has abundant melatonin receptors that induce slowed transit times and harder stool.

Nevertheless, these side effects are generally dose-dependent and reversible, which means most people can safely use melatonin, provided they know appropriate dosing and timing approaches to help mitigate the chance of any digestive complications. The key is starting with lower dosing, optimizing timing of intake, and monitoring the response to your own self-care sleep regimen.

For those who are having digestive issues despite adjusting dosing regimens, research-based methods like therapy for insomnia (CBT-I), optimizing sleep hygiene, or other natural approaches may provide appropriate sleep support without involving the effects on the GI system.

The bottom line is that quality sleep is essential to our overall health and well-being, including our digestive function! A trained health-care provider or specialist, whether through your doctor or other professional, can assist you to identify the best approach for improved sleep without jeopardizing your digestive health.

If you've struggled with persistent sleep issues using many popular approaches without success, it may be time to explore their stomach effects. These evidence-based recommendations may provide hope for those who address the underlying health issues rather than just provide a sleep product that risks aggravating your digestive function. These approaches yield changes without effects on the digestive system.

If you're on medication or supplements and want to understand the potential side effects, read more about supplements like l-theanine or melatonin and what a melatonin hangover means as well as medication like ambien, dayvigo and quviviq. Or if you're ready to try Sleep Reset's unique CBT-I based program, take our free sleep assessment now to begin!

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Dr. Shiyan Yeo

Dr. Shiyan Yeo is a medical doctor with over a decade of experience treating patients with chronic conditions. She graduated from the University of Manchester with a Bachelor of Medicine and Surgery (MBChB UK) and spent several years working at the National Health Service (NHS) in the United Kingdom, several Singapore government hospitals, and private functional medicine hospitals. Dr. Yeo specializes in root cause analysis, addressing hormonal, gut health, and lifestyle factors to treat chronic conditions. Drawing from her own experiences, she is dedicated to empowering others to optimize their health. She loves traveling, exploring nature, and spending quality time with family and friends.

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