To assess the stone-free rate (SFR) subsequent to percutaneous nephrolithotomy (PCNL) in patients with anatomically anomalous kidneys.Cross-sectional study. Place and Duration of the Study: Department of Urology, Sindh Institute of Urology and Transplantation Karachi, from 23 July 2020 till 30 October 2021.Sixty-five patients of renal stone disease with abnormal kidneys, aged 18-60 years of both genders were enrolled in this cross-sectional study. Demographic information like age, gender, stone size, duration of disease, and type of abnormality were noted. After PCNL, stone-free status was determined after 2 weeks of the procedure by performing ultrasound KUB.A total of 65 patients were included in this study with mean age of 36.37 ± 12.86 years [Range: 18-60]. There were 76.9% of males and 23.1% of females. Regarding anatomical malformation, 46.2% were malrotated kidneys, 16.9% were horseshoe kidneys, 16.9% were partial Duplex system, 9.2% had bifid pelvis. Median duration of the disease was 12 (IQR=10). Forty-one patients (63.1%) had single and 24 (36.9%) had multiple number of stones with average size of 3.26 ± 1.14 cm. SFR after PCNL in patients with abnormal kidneys was 70.77% (46/65) while 29.23% (19/65) were observed with residual fragments. Out of 19 cases with residual fragments, 10 (53.2%) had stone size <1 cm and 9 (47.4%) had stone of 1 to 3 cm. Sixteen out of 19 patients with residual stones were treated with ESWL (most required: one session), and re-do PCNL was performed in three cases.PCNL is an effective and safe operation in anatomically anomalous kidneys. For satisfactory outcomes, it requires extreme care and exceptional surgical skill.Malrotated kidney, Duplex system, Kidney anomaly, Horseshoe kidney, PCNL, Extracorporeal shockwave lithotripsy (ESWL).