The primary objective of the present study was to compare the choice of colectomy, i.e. total vs. segmental colectomy, in cases of hereditary non-polyposis colorectal cancer (HNPCC/lynch syndrome), and to assess the efficacy, oncological safety, functional outcome and post-operative complications of total abdominal colectomy with ileorectal anastomosis vs. segmental colectomy in HNPCC. A total of 289 patients who fulfilled the Amsterdam I and II criteria for HNPCC were included in the present study. The criteria for confirmation of the diagnosis were five micro-satellite markers, namely BAT25, BAT26, D2s123, d5S346 and D17S250. Group 1 included those patients who received their diagnosis in the years 2011–2013 and those in group 2 had been diagnosed in the years 2014–2016. The cohort had been subjected to two different types of surgery: i) Standard and extended surgery including total colectomy with ileal pouch anal anastomosis and subtotal colectomy and ii) segmental resection of the colon. Analysis of patient data indicated that in group 1, the extended resection was performed more frequently than in group 2 (68 vs. 34% of cases) and accordingly, segmental resection was less frequent (32 vs. 66%; P<0.001). In conclusion, the extensive rather than the segmental resection has been commonly performed several years ago, but at present, the surgical method of choice in cases of lynch syndrome is segmental resection. Trial registry no. QU/MR2011/CRC5, dated 21 March 2011.