Our aim is to study the prospective trial where urine cytology was used to detect the acute urothelial mucosal damage in patients who undergo extracorporeal shock waves lithotripsy (SWL). The study included 48 consecutive patients (28 male, 20 female) with mean age of 49.02 years (range 18–66) who were treated with SWL due to renal stones (30 patients) or upper ureter stones (18 patients). The mean calculi diameter was 12.44 mm (range 5–20). Urinary cytologic examinations were done for all patients immediately before and after SWL therapy and 10 days latter. The average numbers of transitional cells, red blood cells and myocytes were counted under 40 × magnification. In overall patients the average numbers of transitional cells at the cytologic examinations done immediately before and after SWL therapy were 1.6 and 7.53 cell/field, respectively (p = 0.001). The increment in transitional cells at cytologic examination after SWL was significantly influenced only by number of shock waves applied (p = 0.003). No muscle cell was detected in all cytologic examinations. The cytologic examinations which were done after 10 days of SWL therapy showed recovery from all cytologic abnormalities. The acute increment in number of transitional cells after the SWL is not clinically important and it is a temporary change. Urothelial lesion is limited to mucosal layer and there is no evidence of damage to basal membrane or deeper muscle layer. SWL safety on urothelial and muscular layer was demonstrated. However, evaluation of larger series with use of other lithotripters is necessary before reaching any definitive conclusions.