The purpose of this study was to analyze the various risk factors for urosepsis following percutaneous nephrolithotomy (PNL) and to study the role of 1-week nitrofurantoin before PNL in reducing the risk of urosepsis. All patients undergoing PNL from April 2007 to November 2008 were prospectively included and grouped into four cohorts according to the following inclusion criteria: group A: stones ≤ 2.5 cm, no hydronephrosis, sterile urine; group B: diabetes mellitus, serum creatinine > 2 mg/dl, positive urine culture, stag horn stones, presence of nephrostomy or simultaneous bilateral PNL; group C: stones ≥ 2.5 cm and/or hydronephrosis, sterile urine; group D: similar to group C, but received nitrofurantoin 100 mg bid for 7 days before operation. Preoperative urine culture, intraoperative renal pelvic urine culture and stone cultures were obtained. Fever > 380°C and leukocyte counts > 12,000 were considered as systemic inflammatory response syndrome (SIRS). Endotoxemia was assessed in serum samples. A total of 205 patients were included in the study and grouped into four cohorts as group A (n = 50), group B (n = 54), group C (n = 53) and group D (n = 48). Overall 23% patients had positive renal pelvic urine and/or stone culture, 25% had endotoxemia and 34% developed SIRS. Female gender, chronic renal failure, anemia, hydronephrosis, stones larger than 2.5 cm and prolonged surgery were found to be risk factors associated with urosepsis. Nitrofurantoin prophylaxis resulted in decreased culture positivity (30.2 vs. 8.3%, odds ratio 0.36, p = 0.087), endotoxemia (41.9 vs. 17.5%, odds ratio 0.22, p = 0.001) and SIRS (49 vs. 19%, odds ratio 0.31, p = 0.01). In conclusion, female gender, chronic renal failure, anemia, hydronephrosis, stones larger than 2.5 cm and prolonged surgery were risk factors for urosepsis. Nitrofurantoin is beneficial in the prevention of endotoxemia and urosepsis especially in patients with larger stones and hydronephrosis.