We evaluated the incidence of infectious complications requiring hospitalization after transrectal ultrasound guided prostate biopsy, comparing an augmented regimen of antibiotic prophylaxis to the standard regimen, and established cost-effectiveness at our center. Our standard antibiotic prophylaxis regimen consisted of 3 days of ciprofloxacin or Bactrim™ DS in the perioperative period. An increase in hospital admissions related to infection after transrectal ultrasound guided biopsy from January 2010 through December 2010 led us to initiate an augmented regimen of 3 days of ciprofloxacin or Bactrim DS in addition to 1 dose of intramuscular gentamicin before biopsy from January 2011 to December 2011. Urine and blood cultures along with bacterial susceptibilities were obtained at admission and compared between the 2 groups. Cost analysis was done to determine the cost-effectiveness of standard and augmented regimens. The rate of hospitalization due to post-biopsy infections was 3.8% (11 patients among 290 biopsies) in 2010, which decreased to 0.6% (2 patients among 310 biopsies) in 2011 (p <0.001). Of the admitted patients who received standard prophylaxis, 73% had fluoroquinolone resistant Escherichia coli urinary infection and/or bacteremia and only 9% had strains resistant to gentamicin. Multivariate analysis showed that the standard regimen was significantly associated with hospital admission due to post-biopsy infection (HR 2.078 ± 0.84, p = 0.013). The augmented regimen resulted in a cost savings of $15,700 per 100 patients compared to the standard regimen. The addition of gentamicin to current prophylactic regimens significantly reduced the rate of hospitalization for post-biopsy infectious complications and was shown to be cost-effective.