Colorectal mesenchymal tumors are rare. Therefore, distinguishing between gastrointestinal stromal (GIST) and smooth muscle tumors is important. This study aimed to delineate the immunophenotype and prognostic factors of 75 colorectal mesenchymal tumors. Fifty-three GIST and 22 smooth muscle tumor specimens were included from 1986 to 2007. Forty of 53 GIST were initially diagnosed as smooth muscle tumors and re-diagnosed as CD117 (+) GIST. Immunohistochemical studies were performed with antibodies of CD117, CD34, smooth muscle actin (SMA), desmin, S-100, Ki-67 and PCNA for clinicopathologic and prognostic correlation. In comparison, colorectal GIST exhibited a larger tumor size (P<0.001), higher mitotic count (P<0.001), higher cellularity (P<0.001), less spindle cell type (P=0.004), higher nuclear pleomorphism (P=0.004), and a higher NIH risk (P<0.001) than that of smooth muscle tumors. Positive immunoreactivities of GIST to a panel of antibodies were 88.6% to CD34, 28.3% to SMA, 1.8% to S-100 and 15.1% to desmin. For 75 mesenchymal tumors, survival analyses revealed that older patients (P=0.006), with a large tumor size (P<0.001), high mitotic count (P<0.001), increased NIH risk (P<0.001), non-spindle cell type (P<0.001), high cellularity (P=0.015), high cell pleomorphism (P<0.001), positive Ki-67 (P<0.001), high PCNA (P<0.001) and GIST (P=0.001) had a shorter disease-free survival than that of comparative groups. When the analyses concentrated on 53 GIST, the cell type and cellularity were no longer viable prognostic factors. The tumor mitotic count was the only independent prognostic factor for either mesenchymal tumors or GIST. In conclusion, GIST exhibited heterogeneous characteristics and was significantly larger, more mitotic and a poorer prognostic factor than smooth muscle tumor. The mitotic count is still the most valuable prognostic factor for colorectal mesenchymal tumors after KIT.