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Although shock wave lithotripsy is minimally invasive, earlier studies argued that it may increase patients’ subsequent risk of hypertension and diabetes mellitus. This study evaluated the association between shock wave lithotripsy and new-onset hypertension or diabetes mellitus. The Taiwanese National Health Insurance Research Database was used to identify 20 219 patients aged 18 to 65 years who underwent the first stone surgical treatment (shock wave lithotripsy or ureterorenoscopic lithotripsy) between January 1999 and December 2011. A Cox proportional model was applied to evaluate associations. Time-varying Cox models were applied to evaluate the association between the number of shock wave lithotripsy sessions and the incidence of hypertension or diabetes mellitus. After a median follow-up of 74.9 and 82.6 months, 2028 and 688 patients developed hypertension in the shock wave lithotripsy and ureterorenoscopic lithotripsy groups, respectively. Patients who underwent shock wave lithotripsy had a higher probability of developing hypertension than patients who underwent ureterorenoscopic lithotripsy, with a hazard ratio of 1.20 (95% confidence interval, 1.10–1.31) after adjusting for covariates. The risk increased as the number of shock wave lithotripsy sessions increased. However, the diabetes mellitus risk was similar in the shock wave lithotripsy and ureterorenoscopic lithotripsy groups. Furthermore, the hazard ratio did not increase as the number of shock wave lithotripsy sessions increased. Shock wave lithotripsy consistently increased the incidence of hypertension on long-term follow-up. Therefore, alternatives to urolithiasis treatment (eg, endoscopic surgery or medical expulsion therapy) could avoid the hypertension risk. Furthermore, avoiding multiple sessions of shock wave lithotripsy could also evade the hypertension risk.