To describe the metabolic risk factors and investigate the effect of prophylaxis based on these factors on long-term recurrence of urolithiasis in pediatric patients with hypocitraturia. One-hundred and twenty-nine pediatric patients who underwent percutaneous nephrolithotomy between January 2008 and June 2011 were evaluated for metabolic risk factors. The patients with hypocitraturia were enrolled in this study and the data were analyzed using statistical methods for a mean period of 2 years for metabolic abnormalities, stone type, and the effect of potassium citrate prophylaxis on stone recurrence. A 24-h urine metabolite analysis revealed one or more metabolic risk factors in 115 (89.2 %) of the patients, whereas 14 (10.8 %) of the patients had no metabolic abnormalities. Eighty-two (63.5 %) of 129 patients had hypocitraturia. Of them, 43 (52 %) were male and 39 (48 %) were female, with a mean age of 9.7 +/- 4.9 and 6.7 +/- 4.4 (1-16) years, respectively(p = 0.102). Thirty-five (42.7 %) had pure hypocitraturia, and 47 (57.3 %) had two or more metabolic abnormalities. The most common dual metabolic abnormality was hypocitraturia and hypomagnesuria. Seventy-one patients (87 %) with hypocitraturia received medical prophylaxis and continued regularly, whereas 11 (13 %) patients did not receive medical prophylaxis despite being advised to do so. After a mean follow-up of 26.5 +/- 9.4 months, the rate of recurrence was 1.4 % in the patients with hypocitraturia who continued prophylaxis and occurred in all of the patients who did not receive prophylaxis (p < 0.001). Calcium oxalate stones (95.2 %) were the most commonly found stones in the stone analysis. Detailed clinical and laboratory evaluations should be performed in children with urolithiasis. Appropriate prophylactic treatment as potassium citrate, should be given to prevent reformation of stones in patient with hypocitraturia.