We studied the expression and regulatory effects of ESC self-renewal molecule Nanog in colorectal cancer (CRC). Immunohistochemical analysis of 175 colorectal tumor samples showed that overexpression of Nanog was strongly correlated with poor prognosis, lymph node metastasis and Dukes classification for CRC. Univariate and multivariate survival analyses further indicated that Nanog expression was a potential prognostic factor for CRC. Gain-of-function analysis revealed that lentivirus-mediated Nanog overexpression promoted proliferation, motility and migration of human CRC cells. Interestingly, we found that Nanog played as both an inducer and a receipt of epithelial-mesenchymal transition (EMT) related signals. Nanog induced expression of Slug and Snail, two major regulator of EMT. Meanwhile, Nanog could also be regulated by Snail and initiated by TGF-β1. Our data demonstrate self-renewal gene Nanog has a prognostic role in CRC, which functions in progression of CRC by promoting proliferation, invasion, and motility of human CRC cells, and participates EMT process during CRC progression.