Background Although pilonidal sinus disease is common, development of associated malignancy is very rare. After surgical treatment, most surgeons send the excision material for a histopathological examination. The aim of this study was to examine whether it is necessary to routinely send the pilonidal sinus surgical excision material for this examination. Method The data of 3146 patients were retrospectively screened, and 2486 patients with available histopathological reports of the excision material were included in the study. Results Of the 2486 patients included in the study, 2165 were men and 321 were women, and 94.7% of the patients were under the age of 50 years while 5.3% were 50 years or above. The rate of patients who underwent surgery due to recurrence was 1.2%. No malignancy was detected in any patient after the histopathological examination. Discussion In this study, none of the pathology results was reported as malignant. This confirms that it is necessary to ask the question whether we should routinely send the surgical excision material for a histopathological examination.