We investigated whether previous intraureteral manipulations had an effect on the stone-free rates (SFR) after semi-rigid ureteroscopy (URS) with pneumatic lithotripsy. A retrospective review of all patients who were treated for ureteral stones at two different institutions from June 2003 through January 2010 was performed. Data of 161 URS procedures were analyzed. Stone size, location (distal, mid and proximal) and number (single and multiple), patient demographics and previous intraureteral manipulations were recorded. Patients were grouped as having undergone a previous ipsilateral intraureteral manipulation (Group 1) or not (Group 2). Stone location and number, stone clearance and ancillary procedures were compared. There were no significant differences between Group 1 versus Group 2 for age (p > 0.05), gender (p > 0.05), stone site (p > 0.05) and stone size (p > 0.05). Stones with multiple locations were more frequent in Group 1 (18.5%); however, the difference did not reach statistical significance between the two groups. Similarly, the frequency of multiple stones was also higher in Group 1 (29.6%). Stone site, diameter and gender were comparable in both groups. Stone-free rate of all patients was 84.6% after the first intervention. This rate increased to 98.1% after secondary procedures. Univariate analysis revealed that SFR after URS were low in patients who underwent previous intraureteral manipulations (Group 1:55.6% vs. Group 2:89.1%). SFR after the first intervention were related with stone size, location and number. Additionally, multiple logistic regression analysis indicated a relationship between previous intraureteral manipulations and initial stone clearance rates. Spontaneous passage of stone fragments after URS was associated with stone burden, location, number and previous intraureteral manipulations. Further multiple logistic regression analysis showed that only previous intraureteral manipulations were associated with the expulsion of the stones left for passage.