Objective: National guidelines recommend peri-procedural antibiotics prior to percutaneous nephrolithotomy (PCNL), yet it is not clear which is superior. We conducted a randomized trial to compare two guideline recommended antibiotics: ciprofloxacin (cipro) versus cefazolin, on PCNL outcomes, focusing on the development of systemic inflammatory response syndrome (SIRS) criteria. Methods: Adult patients who were not considered high risk for surgical or infectious complications undergoing PCNL were randomized to receive either cipro or cefazolin perioperatively. All had negative pre-operative urine cultures. Demographic and peri-operative data were collected, including SIRS criteria, intra-operative urine culture, duration of hospitalization, and need for intensive care. SIRS is defined by ≥2 of the following: body temperature < 96.8 °F or >100.4 °F, heart rate > 90 bpm, respiratory rate >20 per minute, WBC count <4000 or > 12,000 cells/mm³. Results: One hundred and forty seven patients were enrolled and randomized (79 cefazolin, 68 cipro). All pre-operative characteristics were similar (p>0.05), except for mean age, which was higher in the cipro group (64 vs. 57, p=0.03). Intra and post-operative findings were similar, with no difference between groups (p>0.05), except a longer mean hospital stay in the cefazolin group (2 hours longer, p=0.02). There was no difference between SIRS episodes on both univariate and multivariate analysis. Conclusions: Despite the relatively broader coverage for urinary tract pathogens with ciprofloxacin, this prospective randomized trial did not show superiority over cefazolin. Our findings therefore support two appropriate options for perioperative antibiotic prophylaxis in patients undergoing PCNL who are non-high risk for infectious complications.