BACKGROUND AND PURPOSE Operative time is an important perioperative factor and is related to postoperative complications and procedural cost-effectiveness. There are few studies, however, investigating factors that affect operative time during percutaneous nephrolithotomy (PCNL). In this study, patient and kidney stone-related factors that influence operative time were analyzed. MATERIALS AND METHODS Clinical records from 1897 patients with renal calculi who underwent PCNL were retrospectively reviewed, and these patients were divided into two groups based on their median operative time (group 1: ≤60 min; group 2: >60 min). Multivariate analyses as well as univariate analyses including chi-square, Fisher exact and Mann Whitney U tests were used to investigate the effects of independent variables on operative time, including patient and kidney stone-related factors such as age, sex, body mass index, history of ipsilateral open surgery, shockwave lithotripsy, presence of hydronephrosis, stone burden, stone type and opacity, and surgical experience. RESULTS The mean operative time was 64.9±27.6 minutes (range 10-220 min). Univariate analyses determined that a history of open surgery, presence of hydronephrosis, stone type and size, and surgical experience correlated with operative time (P<0.05 for all). Multivariate analyses revealed that presence of hydronephrosis (odds ratio [OR]: 1.44, 95% confidence interval [CI]: 1.17-1.78, P=0.002), stone type (OR: 2.12, 95% CI: 1.69-2.70, P<0.0001), stone burden (OR: 2.44, 95% CI: 1.85-3.12, P<0.0001), and surgical experience (OR: 0.56, 95% CI: 0.46-0.70, P<0.0001) were significant independent factors in influencing operative time. CONCLUSIONS Presence of hydronephrosis, renal stone size and type significantly affect the operative time during PCNL. The duration of the operation was also observed to decrease with increased surgical experience.