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Background: To investigate the relevance of two-dimensional (2D) endoanal ultrasonic (EAUS) assessment of anal sphincter and puborectalis morphology by comparison to functional measures derived from patient symptoms and anorectal physiology. Methods: Thirty women (mean age 44 years, mean parity 2) with anal incontinence underwent 2D EAUS, anorectal pull-through manometry, anorectal electosensitivity and sensation to rectal distension, pelvic floor dynamometry, and completed Wexner incontinence scores. EAUS images were reported blind to physiological assessments by a single experienced observer. The external and internal sphincters, and puborectalis were measured and scored for integrity and atrophy, and correlated with symptom load (Wexner score) and physiological data. Results: The mean Wexner score was 10 (range 1–20). The puborectalis could not be accurately measured in 12 patients (44%) on EAUS. Anal squeeze pressure correlated with integrity of the external sphincter (r = −0.4, p = 0.02) but not integrity or atrophy of the puborectalis. There were no other significant correlations between EAUS features and patient symptom load or anorectal physiology (r range, −0.42–0.26, p > 0.05). Conclusion: Two-dimensional EAUS can define sphincter integrity, has a limited role for assessment of muscular quality but is not useful for assessment of the puborectalis.