Objectives. To evaluate the correlation between preoperative urine culture (UC) and intraoperative stone culture (SC) and the impact of SC findings on clinical decisions. Methods. UC and intraoperative fragmented SC were prospectively obtained in all patients undergoing percutaneous nephrolithotomy between January 2004 and March 2005. Patients with a positive UC received a full course of antibiotics before surgery. All postoperative systemic inflammatory response syndrome (SIRS) events were recorded, as was the antibiotic regimen used and any changes in antibiotic treatment secondary to the SC results. Results. The study group consisted of 75 consecutive patients. Of these 75 patients, 33 (49%) had sterile UC and SC results. Both urine and renal stones were colonized in 17 patients (24%); in 6 of them, the UC and SC showed different pathogens. A colonized SC associated with a sterile UC was found in 19 patients (25%). The calculated UC sensitivity, specificity, and positive and negative predictive value for the detection of stone colonization was 30%, 94%, and 84% and 58%, respectively. Seventeen patients (22%) had postoperative SIRS. In 13 of them, a change in antibiotic treatment was made according to the SC findings. On univariate analysis, the incidence of SIRS was not related to the length of the operation, stone-free rate, or supracostal or infracostal access. The relative risk of SIRS when the SC was positive was 3.6. Conclusions. Renal calculi pathogens are one of the predisposing factors for infectious events; however, preoperative UC often fails to grow stone-colonizing bacteria. Intraoperative SC may be essential in directing the antibiotic regimen postoperatively and should be routinely used.