BACKGROUND Anal endosonography is an established technique in the evaluation of anorectal disease. However, it is sometimes difficult to visualize the anterior part of the sphincter complex and anal endosonography may be impossible when anal pain or stenosis is present. The aim of this study was to evaluate vaginal endosonography in the diagnosis of faecal incontinence and perianal sepsis. METHODS Anal and vaginal endosonography were performed in 56 women with faecal incontinence (n = 36) or perianal sepsis (n = 20). The technique and pelvic floor anatomy were described, anal sphincter measurements with anal and vaginal endosonography were compared, and the additive value of vaginal over anal endosonography in the diagnosis of faecal incontinence and perianal sepsis was assessed. RESULTS The pelvic floor was clearly imaged with vaginal endosonography. However, after a relatively short learning curve it was still not possible to image the anal sphincters in three of 28 patients. Except for external anal sphincter thickness, which was significantly lower, all anal canal structure measurements were greater with vaginal than with anal endosonography. Concerning the diagnosis of either faecal incontinence or perianal sepsis, vaginal endosonography added important information in comparison with anal endosonography in 14 (25 per cent) of 56 patients. CONCLUSIONS Vaginal endosonography provides reliable images of the anal sphincters in an undistorted fashion, thereby increasing the diagnostic yield of faecal incontinence and perianal sepsis in 25 per cent of patients. Therefore, endosonographists should become acquainted with this technique.