Melatonin is a naturally occurring hormone that plays a crucial role in regulating your sleep-wake cycle, often referred to as your circadian rhythm. A melatonin deficiency can lead to difficulty falling asleep, staying asleep, or achieving deep, restorative sleep, ultimately resulting in feelings of tiredness during the day and affecting your overall well-being. If you often ever find yourself lying awake before bed or tossing and turning at night, you may already suspect that your melatonin levels are low. However, some more subtle signs and symptoms could suggest your melatonin levels are to blame. Wondering how to spot the problem by other means? These are the nine surprising signs that you have a melatonin deficiency, according to doctors.
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1. Digestive disturbances
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Gastrointestinal issues can have a wide range of underlying causes, so it’s always best to talk to your doctor if you have unexplained discomfort. However, experts say that one surprising cause that easily goes overlooked is melatonin deficiency.
“Low melatonin can impact gut health since melatonin helps regulate digestive rhythms. With low levels, people may experience irregular digestion, bloating, or constipation due to melatonin’s influence on the gut microbiome and digestive motility,” says Raj Dasgupta, MD, Chief Medical Advisor for Sleepopolis.
2. Weakened immune system
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If you notice that you’re getting sick more often than usual during cold and flu season, this could also be related to your melatonin levels.
“Melatonin acts as an antioxidant and immune regulator. Those with a deficiency may notice a higher frequency of colds or infections because the immune system isn’t getting the melatonin boost it typically needs to combat pathogens,” explains Dasgupta.
Resham Uttamchandani, MD, a double board-certified physician, agrees that this is potentially worth flagging with your doctor.
“Melatonin plays a role in immune response by protecting cells from oxidative stress,” she tells Best Life. “A deficiency can lead to a weakened immune system, making the body more vulnerable to infections, illnesses, and prolonged recovery times.”
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3. Skin problems
ShutterstockYou may also be surprised to learn that certain skin issues can be traced back to having low melatonin levels.
“Melatonin supports skin regeneration and repair during sleep. A deficiency may lead to a dull or dry complexion, as skin cells aren’t receiving the regenerative signals from melatonin to maintain healthy skin turnover,” explains Dasgupta.
Uttamchandani adds that melatonin is a “powerful antioxidant” that can help counteract skin damage caused by free radicals or oxidative stress. “Without enough melatonin, the skin may show early signs of aging, such as wrinkles, fine lines, and decreased elasticity,” she notes.
4. Fatigue
ShutterstockIt’s no secret that a melatonin deficiency can compromise sleep. However, sometimes people are unaware that they are waking up multiple times in the night and have to rely on clues they experience throughout the day to piece the puzzle together. Daytime fatigue is one such clue that could suggest a melatonin imbalance.
“Melatonin signals to your body that it’s time to relax and prepare for sleep. Low melatonin levels often cause broken sleep with frequent waking in the night. As a result, people experience a lack of energy during the day and find it difficult to concentrate,” says Hussain Ahmad, MD/MUDr, a UK-based consultant practitioner working with Click2Pharmacy.5. Mood swings
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Mood changes, including heightened anxiety, can also be a sign that your melatonin levels are low.
“Low melatonin can affect mood regulation since poor sleep quality often impacts emotional balance. A lack of melatonin may leave individuals feeling irritable, anxious, or more prone to mood swings, as melatonin influences neurotransmitters related to emotional stability,” says Uttamchandani.
Ahmad explains that when melatonin levels are depleted over a prolonged period of time, this can lead to a build-up of stress hormones like cortisol. “This lack of sleep increases feelings of anxiety, creating a cycle where anxiety itself makes it even harder to fall asleep,” the doctor says.
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6. Irregular menstrual cycles
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If you have a melatonin deficiency, you may also notice that your menstrual cycle becomes less predictable.
“Melatonin levels can affect your menstrual cycle, as they help balance female reproductive hormones. You may experience irregular periods, missed cycles, or more intense PMS symptoms,” says Ahmad.
However, it’s important to note that changes in your cycle can indicate a wide range of other underlying health concerns. Talk to your doctor or gynecologist if you notice that your menstrual cycle undergoes any abnormal changes.
7. Slow wound healing
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According to a 2024 study published in the journal Antioxidants, “melatonin treatment significantly enhances collagen synthesis and promotes accelerated wound healing.” To that end, Ahmad says that slow wound healing can indicate melatonin deficiency.
“Recovery from an injury or surgery is supported by melatonin, which helps control inflammation and boosts immune function. When melatonin is low, your body heals more slowly and scars are more noticeable,” he says.
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8. Increased insulin resistance
ShutterstockSome studies, including one published in 2022 in the journal Biochimie, also suggest that melatonin levels can affect your blood glucose levels, meaning that low levels can put you at heightened risk of high blood sugar.
“Melatonin deficiency impacts your body's ability to process blood sugar, as your cells become less responsive to insulin. This makes it harder to keep your blood sugar stable, especially at night. Over time, this can result in insulin resistance, a key factor in the development of type 2 diabetes,” cautions Ahmad.
9. Frequent headaches
ShutterstockFinally, if you have frequent headaches and you suspect your melatonin levels could be low, it’s worth asking your doctor about a possible connection.
“Melatonin has anti-inflammatory properties and regulates blood flow, both of which help protect against headaches,” explains Uttamchandani. “Low melatonin levels can contribute to more frequent or intense headaches, especially if sleep disruption accompanies the deficiency.”
