Background: The aim of pilonidal cyst surgical treatment is to avoid recurrence of the disease. Aim: To compare the results of Karydakis or Limberg flap for wound closure after pilonidal cyst resection. Material and Methods: Analysis of clinical parameters of patients operated for pilonidal cysts, in which all secondary sinuses and orifices were resected in a block reaching the posterior sacral fascia. The reconstruction technique used (Karydakis or Limberg flap) was according to the surgeon criterion. Results: Of 103 operated patients, in 24 aged 21.4 ± 7.2 years (14 males) the Limberg closure was used and in 49, aged 22.2 ± 6.3 years (26 males), the Karydakis closure was used. Rates of complications were 4.1 and 12.2% for Limberg and Karydakis closure, respectively (p = 0.04). The rates of recurrence were 8.3 and 12.2% respectively (Ns). Conclusions: Karydakis closure technique after pilonidal cyst resection has a higher rate of complications than Limberg closure.