Due to selection bias, the oncologic outcomes of APR and ISR have not been compared in an interpretable manner, especially in patients treated with preoperative CRT. To assess factors influencing oncologic outcomes in patients with locally advanced low rectal cancer treated with preoperative chemoradiotherapy (CRT) followed by abdominoperineal resection (APR) or intersphincteric resection (ISR).Between 2006 and 2011, 202 consecutive patients who underwent APR or ISR after preoperative CRT for locally advanced rectal cancer were enrolled in this study. The median follow-up period was 45.3 months (range: 5-85.2 months). Multivariate and propensity score matching (PSM) analyses were performed to reduce selection bias.Of the 202 patients, 40 patients (19.8%) underwent APR and 162 (80.2%) required ISR. In unadjusted analysis, patients undergoing APR had a higher 5-year local recurrence (P < 0.001) and distant metastasis rate (P = 0.01), respectively. However, the higher local recurrence rate for APR persisted even after PSM, and these findings were verified in the multivariate analyses. Moreover, patients with advanced tumors, as assessed by restaging magnetic resonance imaging and luminal circumferential involvement, had a significantly higher local recurrence rate after APR compared with ISR.This is the first PSM based analysis providing evidence of a worse oncologic outcome after APR compared with ISR. In addition, the results of the subgroup analysis suggest that a more radical modification of the current APR is required in cases of advanced cancer.