Background: The term ‘pilonidal sinus’ (PS) reflects an acute exacerbating, purulent, fistulating chronic inflammation located in the coccyx region. Systematic histological investigations are scarce, and the etiology has remained controversial. Methods: Histological and immunohistochemical characterization of totally excised material of 27 patients (68 specimens) with PS (no antecedent and no current clinical signs of hidradenitis suppurativa, HS) and its correlation with data on HS which we published earlier. Results: Follicular hyperplasia/hyperkeratosis and interfollicular epidermal hyperplasia are main features of PS. Early pathology seems to take place at terminal hair follicles, whereas sinus tract formations are a secondary event. Focused regions show an inflammatory mixed infiltrate consisting of CD3+, CD4+, CD8+, CD68+ and CD79+ cells. Conclusions: PS and HS have various common characteristics at the histological and immunohistochemical level. Considering PS as a unilocalized type of HS, risk factors known in the latter should henceforth be evaluated in PS as well.