BACKGROUND AND AIMS: To evaluate symptom presentation and underlying pathophysiology of colonic/anorectal dysfunction in females with functional constipation (FC) and hypermobile Ehlers-Danlos syndrome (hEDS)/hypermobility spectrum disorder (HSD) METHODS: Case-control study of 67 consecutive female patients with an established diagnosis of hEDS/HSD referred to a specialist centre for investigation of FC (Rome III criteria), age-matched (1:2 ratio) to 134 female controls with FC scoring 0 on the validated 5-point joint hypermobility questionnaire. Symptoms and results of colonic/anorectal physiology testing were compared. An independent series of 72 consecutive females with hEDS/HSD, referred to a separate hospital for investigation of FC, was used to validate physiological findings. RESULTS: Females with hEDS/HSD were more likely to report constipation for ≥ 5 years (76.1% vs. 61.2%, p = 0.035), and a greater proportion had a high Cleveland Clinic constipation score (≥12: 97.0% vs. 87.3%; p = 0.027). The proportions with delayed whole-gut transit were similar between groups (35.3% vs. 41.7%; p = 0.462), as were the proportions with functional or structural abnormalities on defaecography (functional: 47.8% vs. 36.6%; p = 0.127; structural: 65.7% vs. 66.4%; p = 0.916). However, rectal hyposensitivity was more common in those with hEDS/HSD (43.3% vs. 20.1%; p = 0.0006); this was confirmed in the validation cohort (rectal hyposensitivity: 45.8%). CONCLUSIONS: Rectal hyposensitivity is a common pathophysiological factor in females with FC and hEDS/HSD as confirmed in two separate cohorts. The rectal hyposensitivity may be due to altered rectal biomechanics/neuronal pathway dysfunction. Management may be better focused on enhancement of sensory perception (e.g., sensory biofeedback).