Published data on the association between calcium oxalate (CaOx) crystallization and kidney stone disease in children are scarce. The aims of this study were to determine CaOx crystallization using the Bonn Risk Index (BRI) in children with urolithiasis in comparison to healthy controls, to evaluate the relationships between BRI and urinary parameters, such as pH, calciuria, oxaluria and citraturia, and to assess the association between BRI and the size of renal stones. We compared the BRI in 142 Caucasian children and adolescents (76 girls, 66 boys) aged 3-18 years with kidney stones and 210 healthy age- and sex-matched controls without urolithiasis. Urinary ionized calcium ([Ca2+]) was measured using a selective electrode, while the onset of spontaneous crystallization was determined using a photometer and titration with 40 mmol/L ammonium oxalate (Ox2-). The calculation of the BRI value was based on the Ca2+:Ox2- ratio. High-resolution renal ultrasonography was carried out to estimate the size of the renal stones. The BRI values were 15-fold higher in children with renal stones than in healthy children without stones. The same trend was shown by BRI/kg body weight (tenfold greater in children with renal stones than in healthy children without stones), BRI/per 1.73 m2 body surface (13-fold greater) and BRI/body mass index (23-fold greater). No association was observed between BRI and the diameter of stones. Children with kidney stones, both males and females, had an increased BRI compared with subjects without urolithiasis. High BRI suggests an association with lower urinary pH, hypercalciuria, hyperoxaluria or hypocitraturia, which are all risk factors of kidney stones. An increased BRI in children, although unrelated to renal stone size, reflects the risk of calcium oxalate crystallization and may indicate early metabolic disorders leading to urolithiasis.