To investigate and compare the infectious and non-infectious complications of single-dose versus multiple-dose antibiotic therapy for trans-rectal ultrasound (TRUS)-guided biopsy of the prostate. Patients were enrolled in a prospective randomized study that was designed to investigate the effects of single-dose versus multiple-dose antimicrobial prophylaxis regimen mainly on asymptomatic bacteriuria, urinary tract infection (UTI) without fever, fever and urinary septicemia. The single-dose group received one ciprofloxacin 500 mg tablet and two metronidazole 250 mg tablets at 2 hours before the biopsy, while the multiple-doses group received those every 12 hours from 3 days before the biopsy. One-hundred and sixty patients were evaluated in two groups and bacteriuria in urinalysis was encountered in 12 patients (15%) in the single-dose group and four patients (5%) in the multiple-dose group, with a significant difference (P=0.035). UTI without fever occurred in six patients (7.5%) in the single-dose group and one patient (1.25%) in the multiple-dose group, with no significant difference (borderline P=0.053). After biopsy, three patients (3.75%) returned with fever due to UTI and bacteremia in the single-dose group and none in the multiple-dose group, but with no significant difference (P=0.08). Regarding non-infectious complications, there were no significant differences between the two groups. Using prophylactic antibiotics for prostate biopsy in multiple doses, and at least 3 days before the procedure significantly reduces the rate of bacteriuria compared with a single-dose regimen.