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Constipation: Root Causes and Remedies

1/13/2025

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Constipation and gastrointestinal (GI) issues in children are on the rise, creating significant discomfort and frustration for both kids and their families. Increasingly sedentary lifestyles, processed diets, and heightened exposure to medications like antibiotics and acid blockers are just a few of the factors contributing to this growing problem. It’s not uncommon to see children struggling with irregular bowel movements, abdominal pain, bloating, and other digestive challenges, which can affect their mood, energy levels, and even their overall quality of life. 
​Constipation in children can manifest in various ways, even if they are having daily bowel movements. Hard, painful, or incomplete stools may indicate underlying constipation, which can affect a child's comfort and well-being. Often, constipation contributes to urinary issues like urine holding or incontinence because a full rectum can press against the bladder, disrupting its function. These physical discomforts can also lead to behavioral changes, such as irritability, tantrums, or resistance to using the bathroom, as the child associates bowel movements with pain or distress. Parents may notice avoidance behaviors like squatting, leg-crossing, or frequent bathroom trips without results. Recognizing these signs and addressing constipation early is essential to improving a child’s mood, behavior, and overall health.

For parents, watching their child endure these issues can feel overwhelming, particularly when standard interventions fail to provide lasting relief. While temporary remedies can offer much-needed comfort, they often address only the symptoms and fall short of resolving the deeper, underlying causes of constipation.

Understanding and addressing the root causes of constipation is crucial for long-term resolution and overall health improvement. By tackling the reasons behind a child’s digestive struggles, we can ensure not only symptom relief but also the promotion of better GI and overall health. Below, we explore some of the most common and often overlooked contributors to constipation in children.
Root Causes of Constipation

1. Low Acetylcholine Synthesis
One of the less obvious yet significant causes of constipation is a deficiency in acetylcholine, a neurotransmitter essential for proper gut motility. Acetylcholine drives the coordinated muscle contractions of the intestines, known as peristalsis, which move stool through the digestive tract. Low acetylcholine synthesis is often secondary to deficiencies in key nutrients like thiamine (vitamin B1) and riboflavin (vitamin B2). These B vitamins are critical for energy production and proper neurological function, including the synthesis of acetylcholine. Additionally, inadequate choline intake can impair acetylcholine production, as choline serves as a direct precursor for this vital neurotransmitter. Supplementing with choline-rich foods such as eggs, meat, and sunflower lecithin, or using choline supplements like polyenylphosphatidylcholine (PPC) or phosphatidylcholine, can support acetylcholine levels and improve gut motility, helping to address constipation at its source. 


You can read more about acetylcholine synthesis here.

2. Dairy in the Diet
Dairy products are a common dietary contributor to constipation. For some children, the proteins in dairy can be difficult to digest, leading to gut inflammation and slowed intestinal movement. Researchers in Spain, Iran and Brazil have all concluded that cow's milk can be a causative factor for constipation in many children (Bourkheili 2021, Irastorza 2010, Daher 2001). Additionally, dairy products often lack fiber, which is essential for softening stools and promoting regularity.


3. Low-Fiber Diet and Inadequate Fluid Intake
Fiber is vital for healthy digestion, as it adds bulk to stool and helps it move efficiently through the intestines. Unfortunately, many children’s diets are lacking in fruits, vegetables, whole grains, and other fiber-rich foods. When coupled with low fluid intake, this can lead to hard, dry stools that are difficult to pass.
Hydration plays a critical role in digestion, as water helps soften stool and keeps the intestines functioning smoothly. Without sufficient fluids, the body reabsorbs water from the stool in the colon, making it harder and more difficult to pass.


4. Mitochondrial Dysfunction and Hypothyroidism
Both mitochondrial dysfunction and hypothyroidism can lead to low muscle tone (hypotonia), which affects the muscles of the digestive tract. The intestines rely on strong muscle contractions to move stool, and when muscle tone is reduced, constipation often results.
  • Mitochondrial Dysfunction: The mitochondria are the energy powerhouses of cells, including those in the gut. When they are not functioning properly, energy production is impaired, leading to weakened intestinal muscles and slower motility. You can read an in-depth article about thyroid hormone function here: 
    Mitochondria - Why They're Important and What They Need to Function
  • Hypothyroidism: An underactive thyroid slows down metabolism, including the digestive process. This can result in sluggish bowel movements and chronic constipation. You can read an in-depth article about thyroid hormone function here: 
    Pediatric Thyroid Reference Ranges

5. Gastrointestinal dysbiosis
Emerging research suggests that an imbalance in gut microbes, known as dysbiosis, can play a significant role in the development of constipation. (Pan, etal. 2022) For instance, an overgrowth of Methanobrevibacter smithii, a methane-producing archaeon naturally present in the digestive system, has been linked to slower intestinal transit. When M. smithii proliferates excessively, it generates higher levels of methane gas, which can interfere with the coordinated muscular contractions that move food through the gut. This disruption not only delays the passage of stool but may also compromise overall digestive function by affecting nutrient absorption and gut barrier integrity. A comprehensive stool test can be an invaluable tool for detecting dysbiosis, providing crucial insights that enable healthcare professionals to tailor an effective treatment strategy for constipation. Addressing dysbiosis through dietary modifications, probiotics, or other targeted therapies could help restore a healthy microbial balance, potentially alleviating constipation and promoting better digestive health. 

Order a GI Effects® Comprehensive Profile here.

Remedies for Constipation

Addressing constipation effectively involves a two-pronged approach: resolving immediate symptoms while working on the underlying root causes. Remedies can provide relief and improve comfort as you address deeper issues like nutrient deficiencies, dietary factors, or medical conditions. For children, finding gentle, natural, and safe solutions is especially important. Here are some remedies that can help alleviate constipation and promote healthy digestion while supporting overall gut health.

1. Aloe Juice
Aloe juice is a natural remedy known for its soothing properties. It helps hydrate the intestines and acts as a gentle stimulant to improve bowel motility. Aloe also contains bioactive compounds that reduce inflammation in the gut, making it especially helpful for children with sensitive digestive systems. Look for a child-friendly, preservative-free aloe juice, and start with small amounts to gauge tolerance.
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2. Kid-e-Reg Herbal Supplement
Kid-e-Reg is a blend of herbs traditionally used to support healthy digestion and bowel regularity. Its key ingredients include:
  • Slippery Elm: Coats and soothes the intestinal lining, easing irritation.
  • Licorice Root: Supports gut health by reducing inflammation and promoting mucus production.
  • Fennel and Anise: Help reduce bloating and gas while gently stimulating the digestive tract.
  • Fig Syrup: Adds natural sweetness and fiber to aid digestion.
This combination works as a gentle yet effective way to help relieve constipation in children.
3. “Poop Chocolate”
This kid-friendly remedy combines two simple ingredients: dairy-free chocolate and coconut oil, mixed in equal parts. Melt the chocolate chips and coconut oil together over a double boiler or at 30 second intervals in the microwave. Pour mixture into a silicone mold and place in the fridge or freezer. Give your child 1-2 per day. The coconut oil acts as a natural stool softener and lubricant, while the chocolate makes it appealing for children. A small daily serving can help encourage regular bowel movements without harsh stimulants.

4. Magnesium Supplements
Magnesium is a natural muscle relaxant that can help improve gut motility and soften stools by drawing water into the intestines. For children, magnesium glycinate is a safe and effective option. Start with a low dose and gradually increase if needed, under the guidance of a healthcare provider. Magnesium citrate has a stronger laxative effect and can be used as needed when a "clean out" is necessary, but should not be used regularly.

5. Prune or Pear Juice
Prune and pear juices are classic remedies for constipation. They contain natural sorbitol, a sugar alcohol that acts as a gentle laxative. These juices also provide fiber, which supports regularity. Opt for unsweetened varieties, and dilute them with water for younger children.

6. Probiotic Foods or Supplements
Probiotics support healthy gut bacteria, which play a crucial role in digestion and bowel regularity. Foods like dairy-free yogurt, sauerkraut, and pickles (made without vinegar) are great options for kids. Alternatively, high-quality probiotic supplements tailored for children can help restore balance to the gut microbiome. Be careful using probiotics in children who are bloated or have other signs of small intestinal bacterial overgrowth (SIBO) as this can worsen this condition. 

7. Chia Seed Pudding
Chia seeds are a great source of fiber and form a gel-like consistency when soaked in liquid, making them a natural stool softener. Mix chia seeds with dairy-free milk and a touch of natural sweetener to create a kid-friendly pudding that can promote regular bowel movements. 


  • 4 Tablespoons chia seeds
  • 1 cup almond milk or other non-dairy milk
  • ½-1 Tablespoon real maple syrup
  • ¼ teaspoon vanilla extract, optional
  • Toppings of choice: fresh berries or other fruit, granola, nut butter, etc

Mix the ingredients in a covered container or mason jar. Place in refrigerator for about one hour. Mix one more time to ensure chia seeds are evenly dispersed then leave overnight in the refrigerator. Top with your child's favorite topping and enjoy.

8. Massage and Movement
Physical activity stimulates digestion and encourages bowel movements. Incorporating daily movement, such as walking, running, or playing, can be highly effective. Gentle abdominal massage, focusing on the natural flow of the digestive tract, can also help move things along.
9. Vibration Plate
The gentle vibrations from a vibration plate can stimulate the vagus nerve, which plays a crucial role in regulating the digestive system and promoting healthy gut motility. This stimulation also activates the overall nervous system, encouraging relaxation and improved communication between the brain and the digestive tract. By enhancing parasympathetic activity, the exercise plate can help ease constipation naturally and support better bowel regularity.
10. Castor Oil Packs
Castor oil packs can provide gentle, supportive care for children by promoting relaxation and comfort. They are believed to help reduce inflammation, support digestive health, and enhance lymphatic circulation, which can aid in detoxification. Additionally, the soothing warmth of a castor oil pack can calm the nervous system, making it a helpful tool for overall well-being and stress relief.


Castor Oil Pack for Children instructions and supplies - pdf

11. Warm Epsom Salt Baths
Soaking in a warm bath with Epsom salt can help relax the abdominal muscles and promote stool movement. The magnesium in Epsom salts can also be absorbed through the skin, offering additional benefits for digestion. Choose magnesium sulfate, not chloride. Use 1-2 cups in a full or half full bath tub and allow your child to soak and play for at least 30 minutes. This should be done at least 3-4 nights per week to be effective.

12. Hydration Strategies
Encouraging adequate water intake is essential for softening stools and supporting overall digestion. Add a slice of fruit or a splash of natural juice to water to make it more appealing for children who may resist drinking plain water. 


  • Toddlers 1–3 years: Need about 4 cups of fluids per day
  • Children 4–8 years: Need around 5 cups of fluids per day 
  • Older children: Need 7–8 cups of fluids per day

13. Kiwi and Dragon Fruit
Certain fruits, like kiwi and dragon fruit, are excellent natural remedies for constipation. Kiwi is rich in actinidin, an enzyme that aids digestion, as well as fiber to promote bowel regularity. Dragon fruit, particularly the red variety, is high in fiber and contains prebiotics that support gut health. These fruits are not only effective but also colorful and fun, making them an appealing option for children who may resist other remedies.
Conclusion
​Constipation in children is a common but often multifaceted issue, with roots in diet, nutrient deficiencies, gut health, and overall physiology. While it’s important to address the underlying causes, such as low acetylcholine synthesis, dietary habits, or conditions like hypothyroidism, natural remedies can provide immediate relief and comfort. Options like aloe juice, Kid-e-Reg, “poop chocolate,” magnesium, kiwi, and dragon fruit not only support digestion but are gentle and effective for children.
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Remember, each child is unique, and finding the right combination of remedies and root-cause solutions may take some time. Consulting a knowledgeable healthcare provider can be invaluable in developing a tailored approach. By combining symptom relief with deeper investigation into underlying causes, you can help your child achieve better digestive health and overall well-being.
This post contains affiliate links.
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    Dr. Erica Peirson

    Dr. Peirson is dedicated to helping children with developmental and learning challenges reach their fullest potential.

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