Purpose: To determine risk factors for the development of gallstones and the prevalence of related cholecystectomy in children following hematopoietic cell transplantation (HCT). Patients and Methods: A retrospective chart review of 1343 patients aged below 18 years old who survived at least 1 year after HCT from 1969 to 2011 was performed. Multivariate Cox regression models were used to estimate the hazard ratio (HR) of risk factors associated with gallstones. Results: Gallstones developed in 91 patients, a median of 3.5 (range, 0.1 to 30.9) years after HCT at 16.3 (range, 0.8 to 44.2) years of age, with a 40-year cumulative incidence of 11%. At initial diagnosis, 61 (67%) patients were symptomatic and 30 (23%) had incidental gallstones. Risk factors associated with gallstones included autologous transplant (HR = 2.7, P = 0.02), unrelated donor (HR = 2.0, P = 0.05), grade 3 to 4 acute graft-versus-host disease (GVHD) (HR = 2.2, P = 0.03), chronic GVHD (HR = 2.0, P = 0.05), second transplant (HR = 2.3, P = 0.03), diabetes (HR = 2.2, P = 0.05), and estrogen therapy (HR = 1.8, P = 0.03). Fifty-six patients underwent cholecystectomy. The prevalence of cholecystectomy among 853 surviving patients was 5.2%. Conclusions: Childhood HCT patients have an increased risk of developing gallstones.