Background: Surgical site infections (SSI) are among the most frequent healthcare-associated infections. They impose a substantial burden with increased morbidity and exceeding healthcare costs. Risk factors such as age, diabetes, and smoking status are commonly accounted for in the literature, but few studies address gender differences. Methods: Data from the German Nosocomial Infections Surveillance System (Krankenhaus-Infektions-Surveillance-System (KISS)) from 2005 to 2010 were analysed for cardiac, vascular, visceral, and orthopaedic surgery, with a total of 438,050 surgical procedures and 8,639 SSI. Rates of SSI and isolated pathogens were analysed for gender. Results: Women had a lower rate of SSI (SSI/100 procedures) in abdominal surgery than men (2.92 vs. 4.37; p < 0.001). No gender-specific differences were found in orthopaedic and vascular surgery, while women had a higher risk for SSI in cardiac surgery (5.50 vs. 3.02; p < 0.001). Isolated pathogens showed differences for sensitive Staphylococcus aureus and Pseudomonas aeruginosa, which were more frequent in women (both p = 0.007), while coagulase-negative staphylococci occurred more often in men (18.8 vs. 14.0%; p < 0.001). Conclusion: Gender differences in SSI exist and are procedure-specific. The underlying mechanisms need to be further elucidated so that targeted measures for the prevention of SSI can be developed.