Background Whether total extraperitoneal inguinal hernia repair (TEP) is associated with worse outcomes than transabdominal preperitoneal inguinal hernia repair (TAPP) continues to be a matter of debate. The objective of this large cohort study is to compare outcomes between patients undergoing TEP or TAPP. Methods Based on prospective data of the Swiss association of laparoscopic and thoracoscopic surgery, all patients undergoing unilateral TEP or TAPP between 1995 and 2006 were included. The following outcomes were compared: conversion rates, intraoperative and postoperative complications, duration of operation. Results Data on 4,552 patients undergoing TEP (n = 3,457) and TAPP (n = 1,095) were collected prospectively. Average age and American Society of Anesthesiologists score were similar in the two groups. Patients undergoing TEP had a significantly higher rate of intraoperative complications (TEP 1.9 % vs. TAPP 0.9 %, p = 0.029) and surgical postoperative complications (TEP: 2.3 % vs. TAPP: 0.8 %, p = 0.003). The postoperative length of stay was longer for patients undergoing TAPP (2.9 vs. 2.3 days, p = 0.002), whereas the duration of the operation was longer for TEP (66.6 vs. 59.0 min, p \ 0.001) and the conversion rate was higher (TEP 1.0 % vs. TAPP 0.2 %, p = 0.011). Conclusions This study is one of the first populationbased analyses comparing TEP and TAPP in a prospective cohort of more than 4,500 patients. Intraoperative and surgical postoperative complications were significantly higher in patients undergoing TEP. TEP is also associated with longer operating times and higher conversion rates. Therefore, on a population-based level, the TAPP technique appears to be superior to the TEP repair in patients undergoing unilateral inguinal hernia repair.