Karydakis published a large pilonidal series in 1992, reporting a recurrence rate of less than 1% and complication rate of 8.5%. The aim of this study was to compare the outcomes of Karydakis procedure (KP) performed in the lateral versus the prone position in a consecutive series. Ninety-seven consecutive patients undergoing a KP between March 2000 and February 2018 were retrospectively assessed. Patients with disease sinuses or fistulas extending from the midline to either left or right sides only were considered for KP in the contralateral side position. Surgery was carried out for primary pilonidal disease in 71 patients (73%) and for recurrent disease in 26 patients (27%). The majority (62%) of pilonidal tracts veered off from the midline to either the left or right side only. Wound complications, mostly minor skin separation, occurred in 37 patients (38%). Disease recurrence occurred in eight patients (8%). There was no difference between patients who had KP in a lateral position compared with those operated in a prone position regarding wound complications (41% versus 35%, P = 0.675), disease recurrence (9% versus 7%, P = 1.000), mean operating time (64.6 min versus 66.6 min, P = 0.259) and mean length of hospital stay (1 day for both groups). Pilonidal surgery in the lateral position has potential benefits for patient safety, patient comfort and theatre efficiency. The clinical results of this series show that the KP can be performed safely and effectively with the patient in the lateral position for most cases of pilonidal disease.