BACKGROUND AND AIM Unintentional seepage of stool without awareness is common but its pathophysiology is poorly understood. Our aim was to examine the underlying mechanism(s) for fecal seepage. METHODS We evaluated prospectively 25 patients with fecal seepage, by performing anorectal manometry, balloon expulsion, saline infusion, pudendal nerve latency tests, and symptom assessments and compared their data with 26 fecal incontinence patients and 43 healthy controls. RESULTS Predisposing factors for fecal seepage were back injury (7), obstetric injury (6), hemorrhoidectomy (3), pelvic radiotherapy (1), and unknown (8). In the seepage group, the resting and squeeze sphincter pressures were lower (p < 0.02) than healthy controls, but higher (p < 0.002) than incontinent group. During straining, the intrarectal pressure and defecation index were lower (p < 0.05) in the seepage group compared to controls; 72% showed dyssynergia and balloon expulsion time was prolonged (p < 0.01). Threshold for first rectal sensation was impaired (p < 0.002) in the seepage group compared to controls and incontinent group. The seepage group retained more (p < 0.001) saline than the incontinent group but pudendal nerve latency time was impaired (p < 0.05) in both patient groups compared to controls. CONCLUSIONS Anal sphincter function and rectal reservoir capacity were relatively well preserved but most patients with seepage demonstrated dyssynergia with impaired rectal sensation and impaired balloon expulsion. Thus, incomplete evacuation of stool may play a significant role in the pathogenesis of seepage.