Objective To evaluate the of the decision process to perform staged or synchronous bilateral percutaneous nephrolithotripsy (PCNL) in the treatment of bilateral upper urinary tract calculi. Methods Patients with an indication for bilateral PCNL were enrolled in the study from Jan. 2008 to Dec. 2008. The decision to perform staged or synchronous bilateral PCNL was based on the initial side operative time, the changes of hemoglobin level and systolic arterial pressure, the results of blood gas analysis and the patient′s tolerance at the end of initial side operation. The patients were divided into two groups, patients who underwent synchronous bilateral PCNL were in group one. Patients where the PCNL procedure was stopped after the initial side and subsequently underwent staged bilateral PCNL three to six weeks later were placed in group two. The success and complication rates of two groups were compared and analyzed. Results Of 60 planned simultaneous bilateral PCNLs, nine were stopped after the initial side, due to prolonged operative time in four cases, a hemoglobin level ＜100 g/L or the decrease of more than 30 g/L in three cases, a systolic arterial pressure lower than 90 mm Hg or the decrease more than 30 mm Hg in two cases, an arterial blood pH lower than 7.35 or the arterial oxygen saturation lower than 95% in two cases or the patients were intolerant to the surgery in three cases. Between the two groups, the differences of patient gender, age, BMI, preoperative hemoglobin level, the total hemoglobin decrease, the side initiated operation, stone number and second side stone burden were insignificant. However, there were significant differences in the first operative side stone burden, total stone burden, the first operative side operative time and total operative time. The stone-clearance rate was 87.3% in group one and 88.9% in group two. There was no difference in complication rate of two groups. Conclusions Prolonged operative time, large blood loss during the first operation side and patient intolerance are the main causes of staged bilateral PCNL.