Background There are no prospective trials comparing the two main reconstructive options after colectomy for Ulcerative colitis, ileal pouch anal anastomosis and ileorectal anastomosis. An attempt on a randomized controlled trial has been made but after receiving standardized information patients insisted on choosing operation themselves. Methods Adult Ulcerative colitis patients subjected to colectomy eligible for both ileal pouch anastomosis and ileorectal anastomosis are asked to participate and after receiving standardized information the get to choose reconstructive method. Patients not declining reconstruction or not considered eligible for both methods will be followed as controls. The CRUISE study is a prospective, non-randomized, multi-center, controlled trial on satisfaction, QoL, function, and complications between ileal pouch anal anastomosis and ileorectal anastomosis. Discussion Reconstruction after colectomy is a morbidity-associated as well as a resource-intensive activity with the sole purpose of enhancing function, Quality of Life and patient satisfaction. The aim of this study is to provide the best possible information on the risks and benefits of each reconstructive treatment.