Background: Intergluteal pilonidal disease (IPD) is a common chronic disease occurring in the natal cleft of the sacrococcygeal region. This disease may drastically decrease the quality of life, and lead to incapacity for work for up to several months. Various treatment methods are described in the literature, however, each of the methods has its privileges and disadvantages, and no final recommendations are available regarding a superior surgical treatment method. The present study aimed to contribute to filling the gap in the knowledge regarding the superiority of the available surgical techniques used in the treatment of IPD. Methods: The short-term outcomes of two surgical treatment options for IPD, namely the Karydakis procedure (n = 32) and the Marsupialization technique (n = 33), were retrospectively compared. The duration of complete scar formation, the rate of short-term postoperative complications, the persistence of postoperative pain and the recurrence rate during 3-month postoperative follow-up were investigated. The study was based on a retrospective analysis of data extracted from medical records of adult male patients treated for IPD. Results: The Karydakis procedure was found to be superior in terms of all the abovementioned parameters, except for the rate of short-term postoperative complications, where the two surgical techniques showed comparable results. Conclusions: The results of this retrospective study suggest that marsupialization technique could be mostly replaced by the Karydakis procedure in surgical practice. The latter appears to be associated with a faster return to daily activities and more cost effective.