Rectal intussusception (RI) and external rectal prolapse (ERP) are associated with anal sphincter dysfunction. The aim of this study was to examine sphincter function with anal acoustic reflectometry (AAR) in RI and two distinct phenotypes of ERP termed high and low "take-off". A prospective study of patients with RI and ERP attending a tertiary pelvic floor unit. Clinical data, AAR, and conventional anal manometry were analysed according to the Oxford prolapse grade. A total of 108 (102 [94%] female, median age 62 years [range: 26-95]) patients were recruited into three groups according to prolapse grade: Oxford grades I and II (intrarectal RI, n = 34), Oxford grades III and IV (intra-anal RI, n = 35) and Oxford grade V (ERP, n = 39). As the grade of prolapse increased, resting AAR measurements of opening pressure, opening elastance, closing pressure, and closing elastance decreased (p < 0.001). Maximum resting pressure with manometry was reduced in ERP and intra-anal RI compared to intrarectal RI (p < 0.001). However, incremental squeeze function was not different between the three groups with either AAR or manometry (p > 0.05). There were no differences in AAR or manometry variables between grade IV RI (n = 18) and high take-off ERP (n = 20) (p > 0.05). By contrast, opening pressure (p = 0.010), closing pressure (p = 0.019) and elastance (p = 0.022) were reduced in low take-off ERP (n = 19). Increasing rectal prolapse grade is associated with reduced anal sphincter function at rest indicating internal anal sphincter dysfunction. Physiological differences exist between high and low take-off ERP with sphincter function in the former similar to that seen in grade IV RI.