OBJECTIVE To assess the effect and outcome of percutaneous nephrolithotomy (PNL) versus extracorporeal shock wave lithotripsy (SWL) in patients with renal insufficiency. METHODS A prospective randomized clinical study of 104 renal insufficiency patients with renal stones (serum creatinine 2-4 mg/dl and eGFR < 60 ml/min/1.73 m2 more than 3 months) randomized into two groups: Group A underwent PNL; Group B underwent shock wave lithotripsy (SWL). Treatment effects and outcomes compared between the two groups. RESULTS Between Group A of 50 patients and Group B of 54 cases, demographic data showed no statistically significant differences. The stone-free rate was 84% in Group A versus 26.6% in Group B after the first SWL session. After completion of all SWL sessions, the rate was 88.9% for Group B. Comparing pre and postoperative results of Group A, there is significant improvement of serum creatinine concentrations by 9.1% (p = 0.001), significant improvement of creatinine clearance (p = 0.000) and eGFR (p = 0.003). Although regarding Group B preoperatively and 3 months after SWL there is significant improvement by 8.7% (p = 0.0001), which is less than that of Group A, there is also, improvement of eGFR by 6.7% (p = 0.001), which is less than the eGFR improvement in Group A (12.3%). But there is no statistically significant difference is noted for creatinine clearance in Group B (p = 0.09). CONCLUSIONS The outcomes for PNL and SWL in patients with renal insufficiency and renal stones are encouraging as minimally invasive procedures with no negative effects on kidney function.