Molecular-targeted therapy is one of the most promising therapies for patients with advanced-stage colorectal cancer (CRC). However, a wide range of proteins have unknown expression levels in CRC. The purpose of the present study was to determine the expression levels of various proteins related to colorectal carcinogenesis and cancer development. We examined the expression levels of 507 target proteins using a biotin label-based antibody array in 6 human CRC tissues. We also analyzed the clinicopathological features of CRC patients. In CRC tissues, IL-1α, GRO, Glut5, MIG, ICAM-5, VE-cadherin, uPA and Leptin R were increased when compared to levels in normal colon tissues. MPIF-1/CCL23, FGF R5, MIP2, SAA and IL-18 Rβ were strongly upregulated in rectal cancer when compared to the levels in non-rectal cancer. These data suggest that differential protein expression profiles exist under different conditions, including carcinogenesis and CRC localization. Therefore, an exhaustive analysis of protein expression levels using a biotin label-based antibody protein array is a potentially useful tool for identifying novel individual therapies for CRC patients.