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Introduction: The surgical treatment of kidney stones more than 2 cm in size has been vastly simplified with the popularisation of percutaneous nephrolithotomy (PCNL) since the 1980s. However, technological revolution has witnessed miniaturisation of endoscopic instruments claiming more advantages over the usage of conventional instruments. However, the cost of smaller instruments and the higher expertise needed while using these miniature instruments have forced many surgeons to persist with the conventional procedures. Aims and Objectives: This study was intended to evaluate the structural and functional changes occurring in the kidneys after performing standard PCNL. Materials and Methods: Standard PCNL was done in 92 patients with renal stones of more than 2 cm using 25 Fr adult nephroscope. Pre-operative estimated glomerular filtration rate (eGFR) was calculated a day before the procedure and compared with post-operative eGFR estimated at 3 months. Structural changes occurring after PCNL were studied using USG renal morphometry and scarring at 3 months and compared these observations with pre-operative findings. Results: It was observed that the mean eGFR post-operative was 84.48 ± 32.18 ml/min (at 3 months) versus 77.61 ± 30.15 ml/min preoperatively (P < 0.05). The mean change of renal parenchymal thickness on post-operative USG versus pre-operative USG was insignificant (2.19 ± 0.32 cm vs. 2.22 ± 0.34 cm). There was no correlation between age and gender for change in eGFR. A mild positive correlation (correlation coefficient [r] = 0.065) was found between eGFR change and stone burden. Sixteen patients out of 92 were found to have renal scarring (>10% decrease in parenchymal thickness). Conclusions: We conclude that standard PCNL could be performed in indicated patients without apprehensions about functional loss or structural damage due to the procedure.