Comorbidities
If you have Crohn's disease affecting the ileum, or if you have had an ileal resection, you face a higher risk of developing two painful complications that rarely get discussed together: kidney stones and gallstones. Both conditions share a root cause in the malabsorption that comes with ileal dysfunction, yet many patients only learn about this connection after a stone has already formed. Understanding why your body becomes prone to these stones, and what you can do about it, puts you in a stronger position to prevent them.
How Ileal Crohn's Drives Stone Formation
The ileum is the final section of the small intestine, and it handles two jobs that directly relate to stone risk: absorbing bile salts and absorbing fats. When the ileum is inflamed or has been surgically removed, both of these functions suffer, setting off a chain of events that can lead to stones in two different organs.
For kidney stones, the mechanism centers on oxalate. Normally, calcium in the gut binds to oxalate from food, forming an insoluble complex that passes harmlessly in stool. But when fat malabsorption occurs, unabsorbed fatty acids compete for that calcium, binding to it instead. This leaves oxalate free to be absorbed through the colon wall and filtered into the urine, a condition called enteric hyperoxaluria. The result is calcium oxalate kidney stones, the most common type seen in Crohn's patients. Research shows that between 25 and 45 percent of people with Crohn's develop kidney stones, compared to roughly 10 percent of the general population [1]. Studies have also found a positive correlation between the length of ileal resection and urinary oxalate excretion, meaning more extensive surgery translates to higher stone risk [2].
For gallstones, the problem stems from bile salt malabsorption. The ileum is the primary site where bile salts are reabsorbed and recycled back to the liver. When this recycling is disrupted, bile becomes depleted of bile salts and supersaturated with cholesterol, creating conditions for cholesterol gallstone formation. A second pathway involves pigment gallstones: malabsorbed bile acids spill into the colon, where they solubilize unconjugated bilirubin, promoting its absorption and increasing bilirubin secretion into bile [3]. The prevalence of gallstone disease in Crohn's patients is roughly double that of the general population [4].
The Shared Link Between Kidney Stones and Gallstones
A 2017 study examining risk factors for both conditions in IBD patients found that the presence of gallstones increased the risk for kidney stones nearly fivefold (OR 4.87), suggesting these are not independent complications but rather linked outcomes of the same underlying malabsorption [2]. Both conditions trace back to the ileum's failure to properly absorb bile salts and fats. When bile salts are not reabsorbed, you get bile composition changes that promote gallstones. When fats are not absorbed, you get the calcium-oxalate imbalance that promotes kidney stones. Chronic diarrhea, common in active Crohn's, compounds the problem further by causing dehydration and concentrating stone-forming substances in both bile and urine. Patients who have undergone ileal resection face the highest combined risk, because the absorptive surface is permanently reduced.
Prevention Strategies That Address Both Risks
The good news is that several prevention strategies target the shared malabsorption mechanism behind both types of stones. Staying well hydrated is the single most effective step you can take. Adequate fluid intake dilutes urinary oxalate and helps maintain bile flow, reducing stone formation risk in both organs. Aim for enough water to keep your urine pale yellow throughout the day, and increase intake during flares or periods of diarrhea.
Dietary modifications also help on both fronts. A low-oxalate diet reduces the substrate available for kidney stone formation. High-oxalate foods include spinach, rhubarb, beets, and nuts. Calcium supplementation, when timed with meals, can bind dietary oxalate in the gut before it reaches the colon, directly counteracting enteric hyperoxaluria [1]. Magnesium supplements work similarly by forming insoluble complexes with oxalate. For gallstone prevention specifically, your gastroenterologist may consider ursodeoxycholic acid, a medication that improves bile composition and can prevent cholesterol gallstone formation [2].
Keeping Crohn's disease activity under control remains foundational. Active inflammation in the ileum worsens malabsorption, so effective maintenance therapy reduces the downstream risk of both stone types. If you have had an ileal resection, discuss bile acid sequestrants with your doctor, as these can help manage bile acid diarrhea while potentially improving fat absorption.
When to Talk to Your Doctor
If you experience sharp flank pain, pain radiating to the groin, blood in your urine, or sudden intense pain in the upper right abdomen, seek medical attention promptly. These symptoms may indicate a stone that needs treatment beyond prevention. For kidney stones, treatment options range from increased hydration and pain management for small stones to lithotripsy or surgical removal for larger ones. Gallstones causing repeated symptoms typically require cholecystectomy. One long-term study found that the cumulative incidence of cholecystectomy after ileal resection reached 10.3 percent at 20 years [5].
Track your hydration and any flank or abdominal pain patterns in Aidy. If you have ileal Crohn's, this data helps your GI assess your stone risk proactively and adjust your prevention plan before a stone develops.
Sources:
[1] Nazzal, L. et al. "Intestinal Oxalate Absorption, Enteric Hyperoxaluria, and Risk of Urinary Stone Formation in Patients with Crohn's Disease." Nutrients, 2024. https://pmc.ncbi.nlm.nih.gov/articles/PMC10821467/
[2] Fagagnini, S. et al. "Risk factors for gallstones and kidney stones in a cohort of patients with inflammatory bowel diseases." PLOS ONE, 2017. https://pmc.ncbi.nlm.nih.gov/articles/PMC5638235/
[3] Brink, M.A. et al. "Enterohepatic cycling of bilirubin: A putative mechanism for pigment gallstone formation in ileal Crohn's disease." Gastroenterology, 1999. https://www.gastrojournal.org/article/S0016-5085(99)70507-X/fulltext
[4] Fraquelli, M. et al. "Gallbladder bile composition in patients with Crohn's disease." Digestive and Liver Disease, 2014. https://pmc.ncbi.nlm.nih.gov/articles/PMC4077498/
[5] Fagagnini, S. et al. "Cholecystectomy Risk in Crohn's Disease Patients After Ileal Resection: a Long-term Nationwide Cohort Study." Journal of Gastrointestinal Surgery, 2019. https://pmc.ncbi.nlm.nih.gov/articles/PMC6702183/