Your child is gluten-free but still gets daily stomach aches. Here are the 8 most common causes I see (and what actually fixes them) - from hidden gluten to SIBO to stress.
Your child has been gluten-free for months (or years), but they're still complaining about stomach aches. Every. Single. Day.
You're doing everything "right" - reading labels, avoiding cross-contamination, meal planning. So why does their stomach still hurt?
Here are the 8 real causes I've seen after years in gluten-free parenting groups - and what actually helped.
The "Still Getting Glutened" Checklist (Check This First)
Before we dive into other causes, rule out hidden gluten exposure. Even tiny amounts can cause ongoing stomach pain in celiac kids.
Hidden gluten sources parents miss:
✅ Medications & vitamins (not all are gluten-free) ✅ Shared kitchen items (toaster, cutting boards, butter dish) ✅ Play-dough and craft supplies (kids touch, then eat) ✅ School lunch contamination (shared tables, utensils) ✅ Restaurant cross-contact (shared fryers, prep surfaces) ✅ Gluten-free oats (must be certified GF) ✅ Communion wafers at church (many contain gluten) ✅ Lipstick/lip balm (kids lick their lips)
How to test this: Keep a detailed food and symptom diary for 7 days. Note EVERYTHING that goes in their mouth (food, drinks, vitamins, gum, toothpaste).
If it IS hidden gluten: Stomach aches usually improve within 2-3 weeks of eliminating the source.
If it's NOT hidden gluten: Keep reading - it's one of the 8 causes below.
8 Real Causes of Daily Stomach Aches in GF Kids
Cause #1: Lactose Intolerance (★★★★★ Most Common)
Why it happens: Up to 40% of newly diagnosed celiac kids are also lactose intolerant (temporarily or permanently). The villi that digest lactose are damaged by gluten.
Symptoms:
- Cramping 30-90 minutes after dairy
- Bloating and gas
- Diarrhea
- Stomach gurgles
How to test:
- Eliminate ALL dairy for 2 weeks (milk, cheese, yogurt, ice cream, butter)
- Track symptoms daily
- If symptoms improve, dairy is likely the culprit
What actually works:
- Try lactose-free milk first (Lactaid brand) - many kids tolerate this ★★★★★
- Hard cheeses are lower in lactose (cheddar, parmesan) - start here ★★★★☆
- Lactase enzyme pills (take before eating dairy) - works for some kids ★★★★☆
- Switch to dairy alternatives (almond milk, coconut yogurt) ★★★★★
Parent reality: My daughter's stomach aches disappeared within 5 days of cutting dairy. We reintroduced hard cheeses after 6 months with no issues.
Cause #2: Fructose Malabsorption (★★★★☆ Often Missed)
Why it happens: Some kids can't absorb fructose (fruit sugar) properly. When unabsorbed fructose reaches the colon, bacteria ferment it → gas, bloating, pain.
High-fructose foods that trigger pain:
- Apples, pears, watermelon, mangoes
- Dried fruit (raisins, dates)
- Honey and agave syrup
- High-fructose corn syrup (in many GF processed foods)
- Fruit juice (especially apple and pear)
Symptoms:
- Pain 1-3 hours after eating fruit
- Bloating and gas
- Loose stools
- Stomach distension
How to test:
- Eliminate high-fructose fruits for 1 week
- Stick to low-fructose options: berries, bananas, citrus
- Track symptoms
What actually works:
- Choose low-fructose fruits: strawberries, blueberries, oranges, kiwi ★★★★★
- Limit fruit to 1 serving at a time (don't stack multiple servings)
- Avoid fruit juice (concentrated fructose without fiber)
- Pair fruit with protein/fat (helps slow absorption)
Cause #3: FODMAP Sensitivity (★★★★★ Common in IBS Kids)
Why it happens: FODMAPs are fermentable carbs that can cause pain in sensitive kids. Many gluten-free substitutes are HIGH in FODMAPs.
High-FODMAP foods in GF diets:
- Wheat substitutes: Chickpea flour, lentil pasta
- Vegetables: Onions, garlic, broccoli, cauliflower
- Fruits: Apples, pears, cherries, watermelon
- Legumes: Beans, lentils, hummus
- Sweeteners: Honey, agave, sugar alcohols (sorbitol, xylitol)
Symptoms:
- Cramping and bloating after meals
- Gas and burping
- Alternating diarrhea/constipation
- Pain that improves after bowel movement
How to test: This one's tricky - I recommend working with a pediatric dietitian who specializes in FODMAPs.
Basic low-FODMAP swap guide:
- Instead of onions/garlic → use garlic-infused oil (FODMAP-free) ★★★★★
- Instead of chickpea pasta → use rice or corn pasta ★★★★★
- Instead of apples → use strawberries or oranges ★★★★★
- Instead of regular bread → Schär GF white bread (low-FODMAP) ★★★★☆
- Instead of honey → use maple syrup ★★★★★
Parent tip: We did a 4-week low-FODMAP trial with a dietitian. My son's daily stomach aches dropped from 6-7/10 pain to 2-3/10.
Cause #4: SIBO (Small Intestinal Bacterial Overgrowth) (★★★★☆)
Why it happens: Celiac disease can slow gut motility, allowing bacteria to overgrow in the small intestine. These bacteria ferment food → gas, bloating, pain.
Symptoms:
- Bloating that gets WORSE throughout the day
- Pain within 1-2 hours of eating (especially carbs)
- Burping and gas
- Alternating diarrhea/constipation
- Bad breath
How to test:
- Hydrogen breath test (done at GI doctor's office)
- Blood work showing vitamin deficiencies (SIBO interferes with absorption)
What actually works:
- Prescription antibiotics (rifaximin) - most effective ★★★★★
- Low-FODMAP diet (reduces bacterial food source) ★★★★☆
- Prokinetic agents (help gut motility) - talk to GI doctor ★★★★☆
- Elemental diet (for severe cases) - supervised by doctor
Important: This requires medical diagnosis and treatment. If you suspect SIBO, talk to your child's GI doctor.
Cause #5: Constipation (★★★★★ Sneaky Common)
Why it happens: Many gluten-free foods are LOW in fiber. Kids fill up on GF bread, pasta, crackers (all low-fiber) and skip fruits/veggies.
Symptoms:
- Hard, pellet-like stools
- Straining or pain when pooping
- Going less than 3-4 times per week
- Stomach ache that comes and goes
- Loss of appetite
How to test: Track bowel movements for 1 week. Note frequency, consistency (use Bristol Stool Chart), and any straining.
What actually works:
- Increase fiber gradually (too fast = more stomach pain)
- Target: 10-25g fiber/day depending on age
- Add: Fruits, veggies, beans, GF whole grains (quinoa, brown rice)
- More water (8+ cups/day for school-age kids) ★★★★★
- Probiotic foods or supplements (helps gut motility) ★★★★☆
- Daily movement (physical activity helps bowels move) ★★★★★
- Miralax if needed (talk to pediatrician first) ★★★★★
Foods that help:
- Pears (natural laxative effect) ★★★★★
- Prunes or prune juice ★★★★★
- Chia seeds (add to smoothies) ★★★★★
- Flax seeds (ground, in baking) ★★★★☆
Cause #6: Food Additives & Processed GF Foods (★★★★☆)
Why it happens: Many gluten-free processed foods contain additives that can irritate sensitive guts: gums (xanthan, guar), carrageenan, artificial sweeteners.
Common culprits:
- Xanthan gum & guar gum (in GF breads, baked goods)
- Carrageenan (in non-dairy milks, ice cream)
- Sugar alcohols (sorbitol, mannitol, xylitol in "sugar-free" foods)
- Artificial colors & flavors
Symptoms:
- Cramping after eating processed GF foods
- Gas and bloating
- Loose stools
- Symptoms improve on weekends/vacation (when eating less processed food)
How to test:
- Eliminate ALL processed GF foods for 1 week
- Eat whole foods only: meat, fish, eggs, rice, potatoes, fruits, veggies
- Track symptoms
What actually works:
- Cook from scratch more often (I know, I know - but it helps) ★★★★★
- Choose GF brands without gums (Canyon Bakehouse, Simple Mills) ★★★★☆
- Avoid sugar-free products (they're full of sugar alcohols)
- Read ingredient lists (shorter = better)
Cause #7: Anxiety & Stress (★★★★★ Real Gut-Brain Connection)
Why it happens: The gut and brain are connected via the vagus nerve. Stress literally causes stomach pain in kids - especially those managing a restrictive diet.
Triggers:
- School stress (social situations, food anxiety, academic pressure)
- Worry about being "different" with GF diet
- Fear of accidental gluten exposure
- Transitions (new school year, moving, family changes)
Symptoms:
- Stomach pain before school or social events
- Pain improves on weekends/vacations
- "Butterflies" or nausea
- Pain without other GI symptoms (no diarrhea, bloating, etc.)
How to test: Notice patterns. Does pain happen more on school mornings? Before birthday parties? After stressful events?
What actually works:
- Talk about feelings (validate their stress about being GF) ★★★★★
- Relaxation techniques (deep breathing, progressive muscle relaxation) ★★★★☆
- Cognitive behavioral therapy (CBT) (for persistent anxiety) ★★★★★
- Connect with other GF kids (reduces feeling of isolation) ★★★★☆
- Routine and predictability (reduces food anxiety) ★★★★★
Parent reality: My son's stomach aches dropped significantly after we started doing 5 minutes of breathing exercises every morning before school.
Cause #8: Other Food Intolerances (★★★★☆)
Why it happens: Damaged villi from celiac can make kids temporarily sensitive to other foods while gut heals.
Common intolerances in celiac kids:
- Eggs (especially raw/undercooked)
- Soy (in many GF processed foods)
- Corn (common GF substitute)
- Nightshades (tomatoes, peppers, potatoes)
Symptoms:
- Stomach pain 1-3 hours after eating trigger food
- May include: headaches, skin rashes, fatigue
How to test: Elimination diet under supervision of dietitian:
- Remove suspected food for 2-3 weeks
- Track symptoms
- Reintroduce and watch for reaction
What actually works:
- Keep detailed food diary (helps identify patterns) ★★★★★
- Work with pediatric dietitian (ensures balanced nutrition) ★★★★★
- Retest after 6-12 months (many intolerances resolve as gut heals)
Decision Tree: What's Causing My Kid's Stomach Aches?
Start here:
Q: Is your child NEWLY gluten-free (less than 6 months)?
- YES → Most likely: Lactose intolerance or ongoing gut healing
- NO → Keep going
Q: Does pain happen 30-90 minutes after dairy?
- YES → Try eliminating dairy for 2 weeks
- NO → Keep going
Q: Does pain get WORSE throughout the day + lots of bloating?
- YES → Consider SIBO (talk to GI doctor)
- NO → Keep going
Q: Does your child eat lots of fruit, juice, or honey?
- YES → Try low-fructose diet for 1 week
- NO → Keep going
Q: Is your child constipated (hard stools, infrequent)?
- YES → Increase fiber + water
- NO → Keep going
Q: Does pain happen before school/social events but not weekends?
- YES → Likely stress/anxiety component
- NO → Keep going
Q: Does your child eat lots of processed GF foods?
- YES → Try whole foods only for 1 week
- NO → Consider FODMAP sensitivity - work with dietitian
When to See the Doctor (Don't Wait)
See your pediatrician or GI doctor if:
- Weight loss or poor growth
- Blood in stool
- Severe pain (crying, can't do normal activities)
- Vomiting repeatedly
- High fever with stomach pain
- Pain lasting more than 2 weeks despite diet changes
- Waking up at night with pain
Tests they might order:
- Celiac antibody panel (to check if GF diet is working)
- Complete blood count (check for anemia, infection)
- Stool tests (check for infections, inflammation)
- SIBO breath test
- Food allergy testing (if suspected)
- Endoscopy/colonoscopy (if needed to check gut healing)
What Actually Helped Other Parents
From our gluten-free parenting group (real solutions that worked):
Sarah's daughter (age 7): "Stomach aches every day for months. Turned out to be lactose intolerance. Switched to Lactaid milk and almond milk yogurt - pain gone in 1 week." ★★★★★
Mike's son (age 10): "Daily pain even though strict GF diet. GI doctor diagnosed SIBO. 2 weeks of antibiotics + low-FODMAP diet = life-changing." ★★★★★
Jessica's daughter (age 5): "We were feeding her tons of fruit thinking it was healthy. Cut back to 1-2 servings/day (low-fructose fruits only) and pain dropped by 80%." ★★★★★
Tom's son (age 12): "Stress was the culprit. School anxiety about food safety was causing real stomach pain. Weekly therapy + relaxation techniques helped significantly." ★★★★☆
Rachel's daughter (age 8): "Constipation! She was eating mostly GF bread and pasta (low fiber). Added chia seeds to smoothies, more fruit - regular poops = no more stomach aches." ★★★★★
My 30-Day Stomach Ache Elimination Plan
Week 1: Rule out hidden gluten + dairy
- Keep detailed food diary
- Check all products for hidden gluten
- Eliminate ALL dairy (try lactose-free or dairy alternatives)
Week 2: Address constipation + reduce processed foods
- Track bowel movements daily
- Increase fiber gradually (fruits, veggies, chia seeds)
- Cut processed GF foods by 50%
Week 3: Try low-fructose diet
- Eliminate high-fructose fruits (apples, pears, watermelon)
- No fruit juice or honey
- Stick to berries, bananas, citrus
Week 4: Assess and consult doctor if needed
- Review symptom diary - any patterns?
- If no improvement, schedule GI doctor appointment
- Discuss SIBO testing or FODMAP diet trial
FAQ: Daily Stomach Aches in GF Kids
Q: My child has been gluten-free for 2 years. Why do they still get stomach aches? A: Being gluten-free doesn't protect against OTHER food intolerances (dairy, fructose, FODMAPs) or gut issues (SIBO, constipation). Work through the elimination process above.
Q: How long does it take for celiac gut to heal? A: Kids' guts typically heal faster than adults - 6-12 months on strict GF diet. But some kids take 18-24 months. Persistent symptoms deserve medical follow-up.
Q: Can stress really cause stomach pain in kids? A: YES. The gut-brain connection is real. Anxiety triggers physical pain. If pain correlates with stressful events and there are no other GI symptoms, stress is likely a contributor.
Q: Should I try a probiotic? A: Worth trying, but choose a high-quality GF probiotic (Culturelle Kids, Florastor Kids). Give it 4-6 weeks to see if it helps. Probiotics help some kids but not all.
Q: How do I know if it's SIBO vs. just gas? A: SIBO bloating gets progressively WORSE throughout the day (especially after eating carbs). Regular gas comes and goes. SIBO requires hydrogen breath test for diagnosis.
Q: My kid's stomach aches seem worse since going gluten-free. Is that possible? A: Yes - many GF substitute foods are harder to digest (more gums, fiber, different grains). Try whole foods diet for a week to see if symptoms improve.
Q: Can my child outgrow food intolerances? A: Often, yes! Lactose intolerance after celiac diagnosis often resolves as gut heals (6-12 months). Other intolerances may also improve. Retest every 6-12 months under dietitian supervision.
Q: Should I give my child pain medication for stomach aches? A: Talk to your pediatrician. Ibuprofen can irritate the stomach. Acetaminophen (Tylenol) is gentler but doesn't fix the underlying cause. Better to identify and address root cause.
The Bottom Line: Finding the Real Cause
Daily stomach aches in gluten-free kids are frustrating, but they're usually fixable once you identify the cause.
Start with the most common culprits:
- Hidden gluten exposure ✅
- Lactose intolerance ✅
- Constipation ✅
If those don't help, dig deeper: 4. Fructose malabsorption 5. FODMAP sensitivity 6. Processed food additives 7. Stress/anxiety 8. Other food intolerances
Don't try to fix everything at once - change one variable at a time so you can identify what helps.
Work with professionals - pediatric GI doctor and registered dietitian who specialize in celiac/GF nutrition.
Most importantly: You're not alone. Tons of GF parents deal with this. With patience and systematic elimination, you'll figure out what's causing your child's pain.
Your kid deserves to feel good - and you're doing great advocating for them. Keep going.
