Aim: To determine the correlation between urine sampling from different sites, including stones, and also to ascertain which is more predictive of urosepsis. Material and Methods: All patients undergoing PCNL in Government Medical College Hospital, Calicut during the period of one year (from March 2016 to February 2017) who fulfilled our selection criteria were recruited. The samples collected were 1) midstream urine and bladder urine at cystoscopy, 2) renal pelvic urine collected at the time of ureteric catheter insertion 3) renal pelvic urine collected at percutaneous puncture of the pelvicaliceal system and 4) stones which were extracted. The samples were sent immediately for C&S. Patients were monitored for systemic inflammatory response sysndrome (SIRS). Results: Total of 135 cases were suitable for analysis. Midstream urine C&S was positive in 9.63% of cases. Stone C&S was positive in 30.37% and pelvic C&S was positive in 20.74%. Pelvic urine C&S was a better predictor of infected stones than bladder urine C&S. Of the 135 patients 31.9% had SIRS and 4 patients experienced septic shock. Patients with infected stones or pelvic urine were found to be at a relative risk for urosepsis that was at least 10 times greater (p<0.0001). Bladder urine was not a good predictor of SIRS. Stone C&S had a positive predictive value of 0.7, which was the highest. Preoperative dilatation of pelvicalyceal system correlated with infected pelvic urine. None of the patients with urosepsis had positive blood C&S. Conclusions: Positive stone C&S and pelvic urine C&S are better predictors of urosepsis than bladder urine in our study. So, routine collection of pelvic urine and stone for culture and sensitivity is recommended.