The risk for gallstones (GD) in inflammatory bowel diseases and the factors responsible for this complication have not been well established. We studied the incidence of GD in a cohort of Crohn's disease (CD) and ulcerative colitis (UC) patients and investigated the related risk factors. A case-controlled study was carried out. The study population included 634 inflammatory bowel disease (IBD) patients (429 CD, 205 UC) and 634 age-matched, sex-matched, and body mass index (BMI)-matched controls free of GD at enrollment, who were followed for a mean of 7.2 years (range, 5-11 years). The incidence of GD was calculated by dividing the number of events per person-years of follow-up. Multivariate analysis was used to discriminate among the impact of different variables on the risk of developing GD. The incidence rates of GD were 14.35/1,000 persons/year in CD as compared with 7.75 in matched controls (P=0.012) and 7.48/1000 persons/year in UC patients as compared with 6.06 in matched-controls (P=0.38). Ileo-colonic CD location (OR, 2.14), disease duration>15 years (OR, 4.26), >3 clinical recurrences (OR, 8.07), ileal resection>30 cm (OR, 7.03), >3 hospitalizations (OR, 20.7), multiple TPN treatments (OR, 8.07), and long hospital stay (OR, 24.8) were significantly related to GD in CD patients. CONCLUSION: Only CD patients have a significantly higher risk of developing GD than well-matched hospital controls. Site of disease at diagnosis, lifetime surgery, extent of ileal resections, number of clinical recurrences, TPN, and the frequency and duration of hospitalizations are independently associated with GD.