This study was designed to explore the influence of intra-operative perforation on prognosis of low rectal cancer after APR and to investigate the risk factors of perforation. Perforation is not scarce during the procedure of abdominoperineal resection (APR). There is no consensus on perforation rate and related risk factor for APR. Data of 925 patients who received APR for low rectal cancer between January 2000 and August 2008 were reviewed. The intra-operative perforation rate was 7.4 % (68/925). The recurrence rate was 28.6 % in patients with intra-operative perforation compared with 6.8 % in patients with no perforation (P < 0.001); 5-year survival rate in patients with perforation was 41.4 and 66.3 % in patients with no perforation. Univariate analysis showed that intra-operative perforation affected recurrence rate and survival significantly (P < 0.001, P < 0.001); multivariate analysis revealed that intra-operative perforation was an independent prognostic factors for recurrence (RR: 3.087, P < 0.001), while not for survival (RR: 1.331, P = 0.051). Patients aged more than 70 years, T3 tumor and treated by general surgeon had higher perforation rate (P = 0.001, P = 0.004, P = 0.008). Intra-operative perforation affected the prognosis of low rectal cancer after APR significantly. Elderly patient aged more than 70 years, T3 tumor and general surgeon who performed operation were three risk factors of increased perforation rate.