Purpose To analyze the efficiency and cost-utility profile of ureteroscopy versus shock wave lithotripsy for treatment of reno-ureteral stones smaller than 2 cm. Methods Patients treated for urinary stones smaller than 2 cm were included in this study (n = 750) and divided into two groups based on technique of treatment. To assess the cost-utility profile a sample of 48 patients (50% of each group) was evaluated. Quality of life survey (Euroqol 5QD-3L) before-after treatment was applied, Markov model was designed to calculate quality of life in each status of the patients (stone or stone-free with and without double-J stent) and to estimate the incremental cost-utility. Monte carlo simulation was conducted for a probabilistic sensitivity analysis. Chi-square was used for comparing qualitative variables and T student's for continuous variables. Results Shock wave lithotripsy group had 408 (54.4%) and ureteroscopy group had 342 (45.6%) patients. Of them, 56.3% were treated for renal stones and 43.7% for ureteral stones. Ureteroscopy produced slightly higher overall quality of patients' life, but produced a significant higher overall cost per quality-adjusted life year (QALY) than shock wave lithotripsy, exceeding the cost-utility threshold (20,000€/QALY). Sensitivity analysis confirmed results in 93.65% of cases. Difference was maintained in subgroup analysis (ureteral vs renal stones). Conclusions Results suggest that in our clinical setting shock wave lithotripsy has better cost-utility profile than ureteroscopy for treatment of reno-ureteral stones less than 2 cm, but excluding waiting times, in ideal clinical setting, ureteroscopy would have better cost-utility profile than shock wave lithotripsy.