This study quantifies the damage to the internal anal sphincter (IAS) after a rectal mucosal advancement flap for a high transphincteric fistula in 16 patients using 3D-endoanal ultrasound. This was correlated with postoperative incontinence and quality of life scores. The median length of involved IAS preoperatively was 50 % (20-100) and 93.72 % for EAS (47.4-100 %). IAS division did not influence continence (p > 0.05). Continence deteriorated between the pre-, postoperative (p = 0.014) and six-month follow-up (p = 0.005), with no significant differences after one year (p > 0.05). The FIQOL score and SF-36 deteriorated initially, with recovery in all domains except for mental health after one year. Three fistulas recurred (18.75 %).