We previously showed that B cell receptor associated protein 31(BAP31) was significantly upregulated in colorectal cancer compared with normal mucosa epithelia. However, its expression pattern and pathological role in colorectal cancer are not clearly understood. In this study, we investigated whether the expression of BAP31 was associated with the clinicopathological parameters of colorectal cancer. The expression pattern of BAP31 was detected by immunohistochemistry on a tissue microarray in both primary tumor and paired distant normal mucosa samples from 120 consecutive colorectal cancer patients. Furthermore, BAP31 protein expression was also determined in twenty colorectal adenomas and eight liver metastasis samples. There was positive expression of BAP31 in 64.17% of primary tumors and 6.67% in distant normal mucosa (P=0.000). Negative expression of BAP31 was correlated with distant metastasis (P=0.036) and lower tumor differentiation grade (P=0.001). Patients with BAP31-negative expression showed significantly lower overall survival rate (P=0.003) compared to patients with BAP31-positive expression. Our results demonstrate that BAP31 may serve as a candidate prognostic marker in colorectal cancer and negative BAP31 expression may lead to more aggressive invasion of colorectal cancer.