To evaluate whether changing antibiotic prophylaxis from quinolone to penicillin antibiotics has affected infectious complication rates in those men undergoing transrectal ultrasound-guided prostate biopsy (TRUSgpb). This interventional study was designed to determine whether changing antibiotic prophylaxis had any bearing on developing serious infectious complications after taking TRUSgpb. As a secondary aim, we also investigated Clostridium difficile (C. difficile) rates in the same groups of men undergoing TRUSgpb. Men historically received ciprofloxacin 500 mg orally 1 h before their procedure followed by a 3-day course of 500 mg given twice daily (group A). Due to increasing local patterns of antimicrobial resistance to quinolones and concerns regarding potential antibiotic induced C. difficile infection, antibiotic prophylaxis was changed to a penicillin-based regimen comprising of co-amoxiclav 625 mg given orally 1 h before TRUSgpb followed by a three times daily course for 3 days (group B). Excluded from the study were those men given an alternative antibiotic prophylaxis than those given within the two distinct groups due to reasons of previous hypersensitivity reactions and/or clinical decision by the attending Urologist. Comparisons were made between the groups using two-tailed Fisher's exact tests. In all, 119 and 110 men were identified in groups A and B, respectively. Two men in group A (1.68%) developed sepsis after TRUSgpb requiring hospital admission and intravenous antibiotic treatment. The sepsis rate in group B was significantly higher than that of group A (eight of 110, 7.27%; P = 0.036). Escherichia coli was the only organism isolated from our cohort of patients. There were no incidences of C. difficile infections in either antibiotic prophylaxis groups. Ciprofloxacin appears to provide superior prophylaxis than co-amoxiclav in men undergoing TRUSgpb and was not associated with an increased risk of quinolone induced C. difficile infections. Changing antibiotic prophylaxis from a quinolone-based regime may therefore be putting our patients at an increased risk of serious infectious complications after TRUSgpb.