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To assess the clinical effect of miniaturized percutaneous nephrolithotomy (MPCNL) and flexible ureteroscopy lithotripsy (FURL) for the treatment of renal and proximal ureteral calculi of ≤2 cm.A retrospective analysis was carried out on clinical data of 106 patients with kidney or upper urethral calculi. Among these patients, 58 underwent the MPCNL, and 48 received FURL. Stone-free rates, operating time, blood loss, hemoglobin drop, length of hospital stay, complications, and renal damage indexes were compared.The stone removal rates of the FURL and MPCNL groups were 81.25% versus 87.93% (p > .05). Although operating time was significantly shorter in the MPCNL group, hospital stays were significantly shorter in the FURL group. In addition, pooled analysis showed that mean estimated blood loss was significantly higher in the PCNL group but the hemoglobin decline of the FURL group and PCNL group had no significant difference. The PCNL group had no significant difference in complications compared to the FURL group. Differences on the creatinine levels and urea nitrogen levels before the operation and after the operation were not statistically significant.FURL is an effective method for treating renal stone. FURL not only had a similar stone-free rate as compared to MPCNL but also was associated with less blood loss and more favorable recovery time. However, FURL had a longer operative time.