Composition of urinary stones in children from Yucatán, México, is calcium and uric acid. Polymorphisms in VDR and ZNF365 genes have been associated to calcium and uric acid lithiasis, respectively. We evaluated the association of polymorphisms TaqI and FokI of VDR gene and Ala62Thr of ZNF365 gene with the metabolic disorders (MD) in children with urolithiasis (UL). We included 109 children with UL. Creatinine, calcium, phosphorus, magnesium, uric acid, oxalates and citrates were measured in fresh urine. Urinary indices were calculated for determining the MD. VDR and ZNF365 polymorphisms were determined by PCR-RFLP. Genotype frequencies were compared with the frequency of MD and with the averages of excretion of the analytes, using the statistical package STATA 11.0. The most frequent MD were hypocitraturia (35.8 %) and hyperuricosuria (22.9 %). The comparison of genotype frequencies with the frequency of MD did not show significant differences (p > 0.05). The comparison of the urinary excretion averages of analytes with respect to the genotype showed that GG homozygotes have higher concentrations of uric acid and citrate than AG heterozygotes (p = 0.03), and that fF heterozygotes have lower concentrations of citrate (p = 0.009). Hypocitraturia and hyperuricosuria were the most common metabolic disorders. The frequency of MD is not associated with polymorphisms. However, in children with urolithiasis of Yucatan, GG homozygotes excrete higher concentrations of uric acid and citrates, and fF heterozygotes have lower concentrations of citrates.