The aim of this study was to evaluate the prognostic value of circulating tumor cells (CTC) in nonmetastatic rectal cancer patients treated with short-term preoperative radiotherapy. In this single-center trial, 162 patients with rectal cancer after preoperative short-term radiotherapy (5 × 5 Gy) were recruited from January, 2008 to September, 2011. Clearance of CTC was determined in 91 patients enrolled in the molecular analysis. CTC presence was evaluated with real-time reverse transcription polymerase chain reaction assay (qPCR) based on the expression of three tumor genetic markers: carcinoembryonic antigen (CEA), cytokeratin 20 (CK20), and/or cancer stem cells marker CD133 (CEA/CK20/CD133). We found that CTC detection 7 days after surgery was of prognostic significance for the local recurrence (P value = 0.006). CTC detected preoperatively and 24 hours after resection had no prognostic value in cancer recurrence; however, there was a significant relationship between CTC prevalence 24 hours after surgery and lymph node metastasis (pN1-2). We also confirmed a significant clearance of CTC in peripheral blood (PB) 24 hours after surgery. Preoperative sampling is not significant for prognosis in rectal cancer patients treated with short-term radiotherapy. Detection of CTC in PB 7 days after surgery is an independent factor predicting local recurrence in this group of patients.