Pilonidal sinus is known to be common among soldiers but not among Asian individuals. Few reports have discussed the occurrence of pilonidal sinus in the navy. We analyzed the incidence and etiological factors of 12 cases (11 patients, with 1 recurrence) of pilonidal sinus diagnosed between 1998 and 2004 in Japan Self-Defense Force Hospital Yokosuka. All patients were male, and all lesions were in the sacral area. The patients' average age and body mass index were 29.1 years and 27.4, respectively. The surgical procedures used were primary closures (10 cases, 83.3%) and flaps (two cases, 16.7%), and the number of postoperative hospital days averaged 11.8. Pilonidal sinus was not found to be significantly common among Japan Self-Defense Force personnel in general (7 of 11 patients with pilonidal sinus; not significant); however, it was significantly more common among the crew members of Japan Self-Defense Force ships (seven of seven patients; p < 0.05), which suggests that the on-board lifestyle contributes to the occurrence of pilonidal sinus.