Background No clinical trials have been done to guide the surgeon in the optimal technique of draining a pilonidal abscess. The aim of our study was to investigate whether the location of the incision influences wound healing. Methods Electronic records from the surgical database at our 200-bed district general hospital were reviewed for operative technique (midline vs. lateral) for patients who underwent incision and drainage for acute pilonidal abscess between January 2003 and February 2010. These patients were admitted from the Emergency Department with a pilonidal abscess, underwent operative drainage, and returned for follow-up. The main outcome measure was wound healing time. Results Two hundred and forty-three pilonidal abscesses were drained, 134 with a lateral and 74 with a midline incision. All patients underwent simple longitudinal incision. No patient underwent de-roofing, marsupialisation, or closure. Forty-eight patients with midline drainage who returned for follow-up were matched for gender, age, and microbiology culture results with patients who underwent lateral drainage. Almost all were drained under general anesthesia with a median postoperative stay of 1 day. The overall length of follow-up was the same in both groups (P = 0.13). Abscesses that did not heal were followed-up for the same period of time irrespective of incision type (P = 0.48). Abscesses that healed after midline incision took approximately 3 weeks longer than those drained via a lateral incision (P = 0.02). Our study has limitations since it was a retrospective study that did not capture patients whose abscess drained spontaneously or were drained in the emergency department. Conclusions Pilonidal abscess should be drained away from the midline.