Background: Although many methods, either surgical or non-surgical, are being used for the treatment of pilonidal sinus disease (PSD), there is still no consensus as to what constitutes the most appropriate method of treatment. The aim of this study was to compare the outcomes of the Limberg flap (LF), modified Limberg flap (MLF), and Karydakis flap (KF) procedures. Methods: A prospective, randomized study was conducted on 295 patients scheduled for surgical treatment for PSD at the General Surgery Clinic of the Konya Training and Research Hospital in January 2009-May 2010. Patients with recurrent disease, an ASA score higher than III, obesity (BMI > 35 kg/m2), insulin-dependent diabetes, or a drug or alcohol addiction were excluded. The procedures performed were as follows: LF (n = 96), MLF (n = 108), and KF (n = 91). Results: The patients were followed up for a median of 33 months (range 24-41 months). There were more female patients in the LF group. The rate of seroma formation was higher in the KF group (19.8 %) compared to the LF and MLF groups (5.2 and 7.4 %, respectively; p = 0.027). The rate of wound dehiscence was higher in the KF group (15.4 %) compared to the LF and MLF groups (2.1 and 3.7 %, respectively; p < 0.001) as was the incidence of flap maceration (11 % in the KF vs. 1 % in the LF and 3.7 % in the MLF; p = 0.004). The incidence of PSD recurrence was also higher in the KF group (11 %) compared to the LF and MLF groups (6.3 and 1.9 % respectively; p = 0.027). In a multivariate analysis, the presence of seroma, hematoma, and wound infection were independent predictors of recurrence. Conclusions: In our study, LF and MLF procedures were associated with a lower recurrence and complication rate compared to KF. However, more randomized studies comparing different reconstruction methods after PSD excision are needed. © 2013 Springer-Verlag Italia.