The correlation of ERβ/CD44 expression and progression of patients with stage II of colon cancer were explored in this work. A total of 220 paraffin-embedded specimens with stage II colon cancer from 1995 to 2003 were included for assessing ERβ and CD44 by immunohistochemistry in normal mucosa and tumor tissues. Kaplen-Meier method, log-rank test, and the Cox proportional hazards regression model were used to analyze the overall survival data. ROC curve was used to describe the capacity of variables in prognosis prediction. Jackknife method was used to perform cross validation of predictions. The survival rates were significantly different between the patients with high expression and low expression of CD44-tumor tissues (61 % vs. 90 %, p < 0.0001) and between the patients with high expression and low expression of ERβ-tumor tissue (99 % vs. 36 %, p < 0.0001), respectively. In addition, the interaction between expression of ERβ and CD44 was found that the impact of CD44 to the overall survive appeared only when expression of ERβ was low; and the high expression of ERβ-tumor could be regarded as a protective factor for overall survival. This study suggest that low expression of ERβ-tumor and high expression of CD44-tumor are risk factors for overall survival in patients with stage II colon cancer.