Purpose: In previous studies, a lack of antibiotic prophylaxis, smoking and obesity were described as factors that contribute to the development of a surgical site infection (SSI) after pilonidal disease (PD) surgery. In this study, we evaluated whether the volume of the excised specimen (VS) was a risk factor for SSI. Methods: The patients who underwent surgical treatment for PD from January 2010 through December 2011 were retrospectively evaluated in terms of SSI, time off work and healing time. The single and multiple explanatory variable(s) logistic regression analyses were performed. Results: One-hundred and sixty patients were included in the study. SSI occurred in 19 (11.9 %) patients. In the multiple explanatory variable logistic regression analysis, VS was emerged as a risk factor for SSI (OR 18.78, 95 % CI 2.38-148.10; P < 0.005). The healing time and time off work were longer when a SSI occurred (P < 0.001). Conclusions: This study suggests that the rate of SSI after the surgical treatment of PD is higher in patients with a high VS. A SSI significantly prolongs the healing time. Surgeons can use this data for assessing the SSI risk. As a preventive measure, prolonged use of an empiric broadspectrum antibiotic may be beneficial in patients with a high VS. © Springer Japan 2013.