Background: Because of the higher quality of life that the Karydakis flap provides compared to excision-only treatment, it became a recommended closure technique for pilonidal sinus disease. This study aimed to evaluate whether Karydakis flap technique can be performed in potentially infected tissue if the surrounding cellulitis allows wound closure. Methods: 188 patients with pilonidal sinus who underwent excision only (n=91, 48%) or the Karydakis-flap technique (n=97, 52%) were evaluated. The results were reviewed according to the degree of wound contamination, and the effects of closure technique were studied in terms of early wound complications and the duration of hospital stay. Results: In the excision-only group, one patient developed a hematoma (1%) and one patient had cellulitis of the surrounding tissue (1%), which resulted in a 2% complication rate this group. In the Karydakis flap group, wound abscesses were observed in 12 patients (12%). Additionally, four patients (4%) had hematomas, two patients had seromas (2%) and three had other complications. For the Karydakis group, the overall complication rate was 21%, significantly higher than that for the excision-only group (p<0.01). In the Karydakis group, no association was found between complications and the degree of contamination (p=0.36). Conclusions: These data provide evidence that the Karydakis flap technique might be performed even in potentially infected tissue. Although a considerable number of wound-related complications was observed in the Karydakis flap group, the majority of patients had primary healing. Thus, from our viewpoint, the Karydakis flap seems to be a potential alternative to simple excision in infected pilonidal sinus disease. © 2007 Springer-Verlag.