Over the years, prostate biopsy has become the gold-standard technique for diagnosing prostate carcinoma. Worldwide, several million prostate biopsies are performed every year, most commonly using the transrectal approach. Preoperative antibiotic prophylaxis with fluoroquinolones has been shown to be effective for reducing infection rates. However, in recent years, an increase in febrile infection rates after transrectal prostate biopsy (from 1% to 4%) has been reported in retrospective and prospective studies. The predominant risk factor for infection seems to be the presence of fluoroquinolone-resistant bacteria in faeces. Patients at risk of fluoroquinolone resistance should receive carefully selected antibiotics at sufficient concentrations to be effective. Targeted prophylaxis after rectal flora swabbing has been shown to be efficacious compared with empirical antibiotic prophylaxis. Several forms of bowel preparations are under investigation, although none have yet been shown to significantly reduce infection rates. Perineal prostate biopsy is currently being evaluated as a strategy for preventing the inoculation of rectal flora, but limited data support this approach at present.