BACKGROUND: Nephrolithiasis is a well-known extraintestinal complication of adult inflammatory bowel disease (IBD), mainly attributed to hyperoxaluria. In contrast, data for paediatric IBD are limited. The objective of this study was to evaluate renal stone risk in children and adolescents with IBD by analysing urine composition concerning stone promoters and inhibitors and their possible influencing factors. METHODS: In this cross-sectional study, the 24-h urine composition of 107 children and adolescents with surgically untreated IBD compared to 27 healthy controls was analysed regarding the risk of kidney stone development, including an evaluation using the CMC index [(citrate x magnesium)/calcium]. Disease activity, as assessed by the Paediatric Crohn Disease Activity Index (PCDAI), Paediatric Ulcerative Colitis Activity Index (PUCAI), and faecal calprotectin (FC) was investigated as influencing factor. RESULTS: Stone inhibitors were lower in active IBD than in remission (citrate, P = 0.001; magnesium, P = 0.004). The CMC index was also decreased in active disease (P = 0.001), indicating increased urinary lithogenicity in these children. PCDAI and PUCAI were predictors of the CMC index. This proved relevant in the groups IBD, IBD with active disease (B = - 0.072, P = 0.029, adjusted R(2) = 0.114), ulcerative colitis, and ulcerative colitis with elevated FC (B = - 0.095, P = 0.039, adjusted R(2) = 0.388). In patients in remission/with inactive disease and in those with low FC, urine composition did not differ from that of healthy controls in terms of kidney stone risk. Hyperoxaluria was not associated with paediatric IBD. The prevalence of nephrolithiasis was 0%. CONCLUSIONS: Monitoring urine for lithogenic alterations and calculating CMC index in paediatric active IBD could contribute to identifying at-risk patients for later nephrolithiasis early, although childhood stone prevalence is low.