Background Loop ileostomy is widely employed as a defunctioning procedure for left-sided colonic anastomoses. Closure of the stoma carries a risk of morbidity and even mortality. The aim of this prospective trial was to evaluate the ability of stapled stoma closure to decrease the rates of perioperative morbidity. Methods One hundred and nineteen patients (mean age 56.2 ± 5.4 years) underwent two-stage operations for rectal carcinoma with protective loop ileostomy between 2005 and 2008. All patients were randomly divided into two groups: 56 patients had conventional ileostomy takedown, while in the other 63, a functional end-to-end anastomosis was created using a linear stapler. Groups were comparable in terms of age, gender, body mass index, and other parameters. Results Mean time of stoma closure using functional end-to-end anastomosis was 68 ± 7, when compared to 92 ± 11 min ( P  = 0.01) for conventional stoma closure. The overall morbidity rate after ileostomy closure using a stapler was 3.2%: one patient (1.6%) developed a wound infection and self-limited bleeding from the anastomotic line, while another patient (1.6%) had an ileal obstruction caused by adhesions and required additional intervention. Conventional ileostomy closure resulted in a 14.3% morbidity rate: six patients (10.7%) had prolonged ileus, 2 (3.6%) had small bowel obstruction, and 2 (3.6%) had wound infections ( P  = 0.04). Conclusion Functional end-to-end anastomosis reduces operating time and morbidity compared to conventional ileostomy takedown.