To evaluate the frequency and spectrum of lesions of different pelvic floor muscles at endoanal MRI in women with severe faecal incontinence and to study their relation with incontinence severity and manometric findings. In 105 women MRI examinations were evaluated for internal anal sphincter (IAS), external anal sphincter (EAS), puborectal muscle (PM) and levator ani (LA) lesions. The relative contribution of lesions to differences in incontinence severity and manometric findings was studied. IAS (n = 59) and EAS (n = 61) defects were more common than PM (n = 23) and LA (n = 26) defects. PM and LA defects presented mainly with IAS and/or EAS defects (isolated n = 2 and n = 3). EAS atrophy (n = 73) was more common than IAS (n = 19), PM (n = 16) and LA (n = 9) atrophy and presented mainly isolated. PM and LA atrophy presented primarily with EAS atrophy (isolated n = 3 and n = 1). Patients with IAS and EAS lesions had a lower resting and squeeze pressure, respectively; no other associations were found. PM and LA lesions are relatively common in patients with severe faecal incontinence, but the majority of lesions are found in women who also have IAS and/or EAS lesions. Only an association between anal sphincter lesions and manometry was observed.