Background and Aim: The renal stones of any size could be effectively managed through an essential surgical technique known as Percutaneous Nephrolithotomy (PCNL). The large size renal stones with abnormal kidneys imposed additional challenges for PNCL in anomalous kidneys. The present study aimed to evaluate the effectiveness and safety of Percutaneous Nephrolithotomy in malrotated kidneys. Place and Duration: Conducted at Urology department of Mian Gul Abdulhaq Jehanzeb Kidney Hospital Manglawar, Swat for duration of two years (from May 2019 to April 2021). Materials and Methods. This single-centered retrospective study was conducted on 80 patients who underwent percutaneous nephrolithotomy with malrotation kidneys. The individuals with anomalous kidneys and complex calculi were enrolled in this study. These patients had kidneys anomalies such as horseshoe kidneys, crossed fused ectopia, malrotation kidneys, pelvic and complete stone clearance. Posterior or anterior approaches were followed for the procedure after preoperative evaluation in kidney anomalies. Retrograde catheterization was carried out under spinal and general anesthesia with the patients. For all the patients, stone size and clearance were measured. Results: Of the total 80 kidneys anomalies patients, 55 (68.7%) were male and 25 (31.3%) were females. Overall mean age was 35.26 ± 13.51. The stone size varied from 1.3cm to 7 cm. Patients were categorized into two groups based on stone sizes such as group I (1.3-2.5 cm) had 42 (52.5%) and group II (25-7cm) 38 (47.5%) patients. The patients included renal pelvis 19 (23.6%), the pelvic ureteric junction (PUJ) 8 (10%), horseshoe kidneys 2 (2.5%), crossed fused ectopia 9 (11.3%), and malrotation kidneys 3 (3.8%).The stone clearance was completed in 77 (96.3%) patients. The statistically significant factor for complete clearance was the staghorn stone calculus. Conclusion: Percutaneous nephrolithotomy is a safe and effective procedure for large renal stones management in patients of anomalous kidneys. Higher renal stones clearance can be achieved with minimum morbidity by suitable preoperative evaluation and technical experts. Keywords: Malrotated kidney; Nephrostomy, Percutaneous; Nephrolithiasis; Abnormality