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BACKGROUND Huntington's disease (HD) patients often report anorectal dysfunction; however, in HD research no detailed analysis of these complaints has been published. OBJECTIVE To report anorectal dysfunction in a systematically studied cohort of HD subjects. METHODS In 54 HD patients (24 men) and 10 presymptomatic HD mutation carriers (2 men) and in 99 controls (44 men) a history of anal incontinence and constipation was obtained and data was compared accordingly. In HD mutation carriers a clinical neurologic assessment and in some cases anorectal manometry were performed. RESULTS Defecation urgency was reported by 28% of our HD mutation carriers, soiling in 18% and fecal incontinence in 28%. Severe anal incontinence (solid stools) was found in 0% men / 10% women, moderate (liquid stools) in 21% / 13%, and mild (flatus only) in 67% / 47% of our HD subjects. Compared to controls, anal incontinence was significantly more common in HD subjects (p < 0.001). Severe chronic constipation was found in 4.2% men / 0.0% women, moderate in 8.3% / 0.0%, and mild in 21% / 27% of HD subjects. Constipation was more common in HD men (p = 0.02) than in HD women (p = 0.144). Anorectal dysfunction was not reported by 54% of our HD subjects. Patients reporting incontinence or constipation were significantly more depressed (r = 0.53, p = 0.001). Upon anorectal manometry reduced resting anal pressure was found in 4 of 6 HD women. CONCLUSIONS Our study demonstrated significant bowel dysfunction in HD patients. We propose these symptoms to be of central autonomic origin, although we cannot exclude effects of medication. These often neglected symptoms in HD subjects require greater attention from physicians.