The main impetus for a patient with familial adenomatous polyposis to choose colectomy with ileorectal anastomosis over ileal pouch-anal anastomosis is the better functional result. However, does better functional result necessarily translate into better overall quality of life? Previous studies of other diseases have demonstrated no such correlation. This study was performed to determine whether any relationship exists between functional result and quality of life in patients with familial adenomatous polyposis after ileorectal anastomosis and ileal pouch-anal anastomosis. All patients with familial adenomatous polyposis who underwent colectomy with ileorectal anastomosis or proctocolectomy with ileal pouch-anal anastomosis from 1980 to 1998 were studied. Functional data were obtained by questionnaire. Health-related quality of life was assessed by two validated instruments, the SF-36 Physical and Mental Health Summary Scales and the SF-36 Health Survey, which measure physical and mental functioning and eight separate health-quality dimensions, including health perception, physical and social functioning, physical and emotional role limitations, mental health, bodily pain, and energy or fatigue. Data were obtained in 44 of 68 patients, 14 with ileorectal anastomosis and 30 with ileal pouch-anal anastomosis. No differences were demonstrated between the two groups for patient age, mean follow-up time, and mean patient age at operation. Functional results were worse for the ileal pouch-anal anastomosis group vs. the ileorectal anastomosis group in number of bowel movements per day (7.5 vs. 5.2; P < 0.05), leakage (43 vs. 0 percent; P < 0.01), pad usage (17 vs. 0 percent; P < 0.01), perianal skin problems (33 vs. 7 percent; P < 0.01), food avoidance (80 vs. 43 percent; P < 0.01), and inability to distinguish gas (37 vs. 7 percent; P < 0.01). Results of the health-related quality-of-life surveys, however, demonstrated no difference between the ileal pouch-anal anastomosis and ileorectal anastomosis groups. The Physical and Mental summary scales for the ileal pouch-anal anastomosis and ileorectal anastomosis groups were not significantly different (Physical Health Scale, 50.3 vs. 50.9; Mental Health Scale, 51.7 vs. 49.6), and none of the eight dimensions of the SF-36 health survey demonstrated statistical differences between the ileal pouch-anal anastomosis and ileorectal anastomosis groups. Better functional results were not equated with better quality of life in this pilot study. Although patients with the ileorectal anastomosis have better functional results than those with ileal pouch-anal anastomosis, the measured health-related quality of life as determined by a validated generic health-related quality-of-life instrument is the same for both groups. These results suggest that all patients with familial adenomatous polyposis might be optimally treated with an ileal pouch-anal anastomosis. More importantly, this study suggests that health-related quality of life should play a greater role in the evaluation of care and treatment in colon rectal surgery.