BACKGOUND: To evaluate the role of neoadjuvant chemoradiation therapy (nCRT) in locally advanced rectal cancer, we retrospectively analyzed the prognosis and survival in patients treated with and without nCRT, and explored the possible mechanisms of chemoradiation resistance. METHODS: Clinicopathologic data of 304 nCRT cases and 301 paired non-nCRT cases were collected. LoVo and HCT116 cell lines were treated with irradiation and chemotherapeutic drugs, and subsequently the expression levels of metastasis-related proteins before and after treatments were compared. FINDINGS: After nCRT, pathologic complete remission (pCR), partial remission (pPR), stable disease (pSD), and progressive disease (pPD) were observed in 26(8.55%), 127(41.78%), 137(45.07%), and 12(3.95%) patients, respectively. Mucinous adenocarcinomas (MC) occurred more frequently in nCRT than in non-nCRT patients (χ2=29.352, P=0.000) and the prognosis in MC patients was worse than that in non-MC patients (χ2=24.617, P=0.000). The difference of survival rates from three to eight years between the nCRT and non-nCRT groups increased gradually. The difference in survival time had statistical significance for 60 days (χ2=5.357, P=0.021) and 70 days (χ2=18.830, P=0.001) rest interval time. T stage, lymph node metastasis, recurrence and/or distant metastasis, and Duke's stage were associated with poor survival. On multivariable analysis, 60 days rest interval, Duke's stage, and recurrence and/or distant metastasis remained significant predictors of survival. Radiation and chemotherapeutic treatment induced polyploid giant cancer cells (PGCCs) formation, and the PGCCs and their daughter cells exhibited strong migratory, invasive, and proliferation abilities. INTERPRETIATION. Radiation and chemotherapy can induce the formation of PGCCs with cancer stem cell properties. PGCCs and their budding daughter cells display strong migration and invasion abilities, which may be related to the poor prognosis in patients with nCRT. Funding: This work was supported in part by grants from the National Natural Science Foundation of China (81472729 and 81672426), and the foundation of committee on science and technology of Tianjin (17ZXMFSY00120 and 17YFZCSY00700). Declaration of Interest: All authors declare no competing interests. Ethical Approval: Our hospital review board approved the use of data from the colorectal cancer database.