Purpose: Pathological complete response (pCR) after neoadjuvant chemoradiotherapy is a favorable prognosticator in rectal cancer patients. We investigated whether the biological features of the primary tumor affect pCR. Materials and Methods:Forty-six patients treated with capecitabine-oxaliplatin and pelvic conformal radiotherapy were considered. Forty-three patients underwent surgery, and the pathologic response was scored according to the tumor regression grade (TRG) scale. Epidermal growth factor receptor (EGFR), vascular endothelial growth factor, poly(adenosine diphosphate-ribose) polymerase-1, X-ray cross-complimenting, thymidylate synthase (TS) and Ki67 expression were evaluated by immunohistochemistry on rectal biopsies obtained before chemoradiotherapy, and scored as the percentage of positive cells. Cutoffs were selected based on ROC analysis. The correlation between the biological factors and the TRG coded as TRG1 (pCR) versus TRG ≧2 (no pCR) was assessed by the χ2 test and logistic regression analysis. Results: Low EGFR (p = 0.007), high TS (p = 0.002), and high Ki67 (p = 0.05) were strongly associated with pCR. Upon univariate analysis, TRG significantly affected disease-free survival (p = 0.03). Conclusions: pCR was significantly associated with high TS, high Ki67 and low EGFR expression. Patients with pCR have a significantly lower incidence of relapse.