The APPEAR procedure was developed to allow sphincter-preserving rectal resection for both benign and malignant pathology, which would traditionally require abdominoperineal excision or completion proctectomy, if treated by conventional means. This clinical trial (clinicaltrials.gov: NCT00534131) evaluated the short-term clinical and physiological results of this procedure. Fourteen patients were enrolled, 7 with neoplasia, 5 with ulcerative colitis, and 2 with traumatic rectal damage. Patients were evaluated preoperatively, and at a median of 2 years after surgery. Nine of 14 patients underwent ileostomy reversal and were followed up for a minimum of 1 year, with 1 patient awaiting closure. Four patients have not yet been considered for ileostomy reversal due to anastomotic perineal fistulae. Transient sexual dysfunction was noted in 3 of 14 patients, but no urological problems occurred. When the APPEAR procedure was performed for neoplasia or trauma, postoperative median Wexner continence score was 5 (range 0-8, n = 6), with a median defecation frequency of 3 (range 1-8/day). All cancers were completely excised with no local recurrence. Following APPEAR with restorative proctocolectomy for ulcerative colitis, median Wexner continence score was 2 (range 0-6, n = 3), with a median daily defecatory frequency of 3 (range 1-5). Preoperative SF-36 scores did not change significantly following ileostomy closure, and anorectal physiological testing was unaltered following perineal dissection. The APPEAR procedure provides an alternative technique to effect an ultra-low sphincter-saving anastomosis, when this is not possible by conventional surgery. Morbidity was encountered and greater experience will be required to fully assess this approach. Nevertheless, this is a promising new procedure with the potential to reduce the need for a permanent stoma even further than is currently the case.