Fecal incontinence (FI) occurs in up to 20% of diabetes mellitus (DM) patients. Rectoanal inhibitory reflex (RAIR) is an enteric anorectal reflex that reflects the integrity of mechanisms in the physiology of FI. We aimed to investigate whether diabetic patients with FI, not constipation, had prolongation of RAIR and altered gut-specific autonomic tone. In this prospective case-matched study 31 type I DM (19 FI and 12 constipation) and 42 type II DM (26 FI and 16 constipation). Another 21 participants were included as controls. Patients underwent the following assessments: cardiovagal autonomic tone (Modified Mayo Clinic composite autonomic severity score), rectal mucosal blood flow (RMBF) (assessment of gut-specific autonomic tone) and RAIR. Three phases of RAIR and the amplitude of maximal reflex relaxation were compared between groups. All participants completed symptom scores for FI and constipation. RAIR recovery time back to resting pressure was slower in diabetic patients with FI than controls (8.7 s vs 3.6 s, P < 0.05) and was an independent variable correlating with symptoms of FI (P < 0.05). RAIR recovery time was correlated with RMBF (r = 0.58, P = 0.04). RAIR is correlated with anorectal symptoms of FI and was associated with gut-specific autonomic neuropathy.