It is common belief that patients failing chemoradiation therapy (CRT) for squamous cell cancer of the anus (SCCA) can be salvaged with subsequent surgery. The aim of this study was to examine our experience with abdominoperineal resection (APR) in cases of persistent or recurrent SCCA with an emphasis on survival and morbidity. All patients between 1985 and 2001 undergoing salvage APR were reviewed. Details of CRT, surgery, tumor characteristics, postoperative complications, and survival were obtained from medical records. There were 22 patients (13 women, 9 men) with a mean age of 62 years (range=42-87). Initial tumors were AJCC stage 2 (16 cases), 3A (3 cases), and 4 (1 case). Mean radiation dose was 47.6 Gy (30-60) and most received concomitant 5-FU. In 20 patients, APR was felt to be "curative" but only 13 (65%) had negative margins on final pathology. Thirteen (59%) perineal wounds broke down with a median time to healing of 7 months. Tumor differentiation (p=0.02) and positive resection margins (p=0.004) were significantly associated with DFS (5-year DFS of 37%). Salvage APR in patients with poorly differentiated tumors or positive resection margins has a high morbidity and poor survival and may warrant a planned APR after CRT instead.