This retrospective study was designed to compare prognostic relevance of magnetic resonance imaging (MRI) findings before and after neoadjuvant chemoradiotherapy (CRT). From 2002 to 2010, 399 patients who underwent surgery after CRT for rectal cancer (≥T3) and had adequate pre-CRT (mr) and post-CRT (ymr) MRI findings were examined. Factors examined included tumour (T), lymph node (N), mesorectal fascia (MRF), extramural venous invasion (EMVI), and tumour regression grade (TRG). Two Cox proportional hazard models were created using mr and ymr findings separately for overall survival (OS), disease-free survival (DFS), and local recurrence rate (LRR). Among mr findings, only mrEMVI was a significant prognostic factor for OS and DFS. Among ymr findings, ymrN, ymrMRF, and ymrEMVI were significant prognostic factors for OS and DFS, whereas ymrMRF and ymrEMVI were significant prognostic factors for LRR. C-indices tended to be higher for ymr findings than for mr findings (OS, 0.682 vs. 0.635; DFS, 0.660 vs. 0.631; LRR, 0.701 vs. 0.617). Survival outcomes of patients having all ymr risk factors were significantly poor (5-year OS, 52.4%; 5-year DFS, 38.1%; 5-year LRR, 27.7%). ymr findings showed better prognostic significance than mr findings. Among ymr findings, ymrN, ymrMRF, and ymrEMVI were independent prognostic factors for oncologic outcomes.