Sacrococcygeal pilonidal sinus disease (SPSD) is a common disorder. None of the current treatment methods seems to be the ideal treatment for SPSD. In this study, we evaluated the effectiveness of polyphenols produced from the components of natural organic matter in soil in the treatment of SPSD. One hundred and ninety two patients with SPSD who used topical polyphenols for the treatment of their disease were studied retrospectively. Information on the characteristics of patients and treatment and results of treatment were obtained from the patient files and/or by telephone surveys. The median duration for total treatment was 12 weeks and the mean follow up period was 22 months. One hundred and sixty six (86.5%) patients got benefit from the treatment. Fifty one (26.6%) patients had minor temporary side effects. In 64 (33.3%) patients SPSD relapsed. Patients were able to continue their normal daily activities during the treatment period and there was no loss of work days. Locally applied natural polyphenols are one step in the direction of finding an ideal treatment of SPSD. They are easy to apply, cheap, safe and associated with a low risk of complications. Their use was not associated with time off work, unnecessary hospital stay or any anatomical distortion of the natal cleft.