We investigated 683 children with nephrolithiasis and 6,498 children without nephrolithiasis aged <3 years. Nephrolithiasis was diagnosed by renal ultrasonography in hospitals in Beijing in September/October 2008. In addition, data was collected on current and past formula feeding and on other possible risk factors for nephrolithiasis. Daily intake of melamine per kilogram of body weight was calculated for each individual. In general, the adjusted odds ratios between melamine dose and nephrolithiasis increased with an increasing daily level of melamine intake per kilogram of body weight. The risk of nephrolithiasis also increased with the increasing duration of exposure. Preterm infants, urinary malformation, and parents with a history of urinary stones were independent risk factors. In children exposed to melamine levels <0.2 mg/kg per day, the adjusted odds ratio expressing the risk for nephrolithiasis was still 1.7 times higher than in those without melamine exposure. These findings suggest that the risk of melamine-induced nephrolithiasis in young children starts at a lower intake level than the levels recommended by the World Health Organization.