We previously reported that the incidence of surgical site infection (SSI) after radical cystectomy was 33% between January 1996 and December 2003 at Sapporo Medical University Hospital. Base on that result, we modified perioperative management for surgical wounds after January 2004. The modifications included the method of suturing and standardization of the period for removal of closed drains and surgical dressings. This study compared the incidence of SSI between the former and latter periods, and assessed risk factors for SSI. The study consisted of 109 patients between January 1996 and December 2003 (Group A), and 104 patients between January 2004 and December 2007 (Group B), who underwent radical cystectomy and urinary diversion or reconstruction. The incidence of SSI was reduced from 32.1% in Group A to 18.2% in Group B (p = 0.027). Methicillin-resistant Staphylococcus aureus (MRSA) was isolated from SSI wounds in 40.0% of patients in Group A and 42.1% of those in Group B. Preoperative MRSA bacteriuria was the only risk factor for SSI in both groups. The incidences of SSI in patients who had such bacteriuria were 45.4% in Group A and 50.0% in Group B. Modification of perioperative management for the surgical wound was partly responsible for the reduction of the incidence of SSI. In conclusion, MRSA is still the main isolated pathogen of SSI after radical cystectomy and this clinical problem remains a challenge to urologists. Effective countermeasures are needed for MRSA bacteriuria involved in the development of SSI.