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5 Signs of Poor Gut Health in Kids

Published January 30, 2024

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When the body’s gastrointestinal system is not in balance, it can manifest as a variety of frustrating symptoms such as gas, bloating, constipation, diarrhea, as well as broad health complaints including fatigue and lowered immunity. Recognizing signs of poor gut health in kids is essential for addressing underlying issues and promoting their digestive health. Here are five signs of poor gut health in kids parents should look out for along with a few expert tips to help re-establish gut health in their little ones. 

1. Digestive Discomfort and Irregular Bowel Movements

The gut microbiome contains trillions of live bacteria that influence metabolism, gut health, nutrient absorption, and immunity. [1]. Disruptions and imbalances to the gut microbiome have been linked to conditions such as irritable bowel syndrome and allergies. Kids experiencing symptoms of frequent digestive discomfort such as bloating or irregular bowel movements might indicate an imbalance in their gut flora. A gut imbalance, or dysbiosisis a commonality in many childhood disorders such as autism, failure to thrive, nutritional disorders, and coeliac disease [2]. Dysbiosis can be caused by a variety of factors such as:

  • Oral antibiotics

  • Medications such as laxatives or NSAIDS

  • C- Section Births 

Begin Health Expert Tip

Encouraging a fiber-rich diet that includes prebiotic-rich fruits and vegetables such as apples, berries, and carrots can help rebuild a balanced gut microbiome by feeding the good bacteria in the gut. For our pickier eaters, Begin Health's Growing Up Prebiotics can offer an extra fiber boost to help bridge the fiber gap in your little one’s diet. It’s tasteless, textureless, and provides 3g of fiber per serving. 

2. Recurrent Digestive Issues or Food Intolerances

Gastrointestinal conditions such as inflammatory bowel disease, Crohn’s Disease, or ulcerative colitis can increase the risk for food sensitivities. Persistent digestive issues from these conditions such as recurrent stomachaches or food intolerances, could also signal gut health imbalances [3].

Begin Health Expert Tip

Consider adding probiotic-rich foods like yogurt and kefir in your little one’s diet to restore a healthy balance of gut bacteria. Studies reveal that probiotics, specifically strains that include bifidobacteria and lactobacillus, can help support the balance of gut microbiota by colonizing in the human intestine and maintaining the stability of the intestinal environment to reduce the risk for food allergies [4]. 

3. Frequent Illness or Weak Immune Response

Up to 80% of immune cells live in the gut microbiota [5]. Therefore, the integrity of the gut can influence overall immunity and the risks for illnesses. Kids with poor gut health could potentially frequent higher rates of illnesses due to a compromised immune system. 

Begin Health Expert Tip

Growing Up Prebiotics contains only two-ingredients: chicory root fiber and human milk ogliosaccharides, which can support immunity in kids by promoting a diverse gut microbiome and help reduce gut inflammation. Consuming prebiotics daily and consistently can help your little one get  the additional immune support they need to stay healthy. Need more tips on immune support for your kids? Check out thesekid’s immunity tips from a Pediatrician.

4. Mood and Behavioral Changes

Poor gut health can also impact your kiddo’s mood and behavior. Serotonin, known as the "happy hormone," is primarily produced in the gut and influences mood, sleep, and appetite. Disruptions in the gut microbiota can interfere with the production and signaling of these neurotransmitters, contributing to mental health disorders [7]. 

Begin Health Expert Tip

Encouraging the consumption of foods rich in omega-3 fatty acids like salmon or flaxseed can also be another way to positively impact mood through diet changes. Studies reveal that omega-3 fatty acids can reduce the risk for common mood disorders such as depression [8]. 

5. Skin Issues or Eczema 

Many studies have shown a two-way relationship between gastrointestinal and skin health [8, 9]. Dysbiosis of the gut is associated with an altered immune response that can potentially increase the risk of eczema. Studies also reveal that atopic dermatitis, or eczema, is associated with lower levels of gut bacterial diversity and lower levels of good bacteria such as bifidobacterium.

Begin Health Expert Tip 

Skin conditions such as eczema are caused by inflammatory responses in the body.  Our Kiddo Poop Test is made for parents who are looking for a more in-depth analysis of the bacteria in their kid’s microbiome to determine the source of inflammation. A personalized gut health report can provide additional information on the bacteria levels in their kid and help parents take action to prevent or reduce inflammation in the body. For more information regarding our Kiddo Poop Test, check out our blogKid’s Gut Health Test: What a Poop Test Can Reveal for Parents.


Signs of poor gut health in kids include irregularity, digestive discomfort, frequent illness, mood or behavioral changes, and skin issues like eczema. Diversifying your kiddo’s food intake with probiotic andprebiotic-rich foods such as kefir, fermented foods, berries, and carrots can help restore microbiome balance and help promote a healthier gut. 


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[8] Mehdi S, Manohar K, Shariff A, Kinattingal N, Wani SUD, Alshehri S, Imam MT, Shakeel F, Krishna KL. Omega-3 Fatty Acids Supplementation in the Treatment of Depression: An Observational Study. J Pers Med. 2023 Jan 27;13(2):224. doi: 10.3390/jpm13020224. PMID: 36836458; PMCID: PMC9962071.

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