Background: Molecular tumor profile assays (MTP) may predict the primary site of origin in CUP, but the impact of site-specific therapy on outcomes is undefined. Accurate identification of CUP patients (pts) with a colorectal site of origin would be expected to improve treatment results by directing the use of colorectal cancer regimens rather than empiric CUP regimens. Methods: We identified CUP patients with colorectal genetic signatures from 213 paraffin-embedded biopsies tested with mRNA-based RT-PCR molecular assays (42 from MDA tested with Veridex assay and 171 from SCRI tested with bioTheranostics CancerTYPE ID assay). Pts with a molecular colorectal cancer profile (most treated with colorectal cancer regimens) were examined for clinical features, results of standard pathologic evaluation including immunohistochemistry (IHC), response to therapy, and survival. Results: The MTP were successfully performed in 185 of 213 specimens (87%) and 32 (17%) had colorectal genetic signatures (Veridex assay 11, bioTheranostics assay 21). All 32 patients had carcinoma (29 with adenocarcinoma); colonoscopy was normal in the 30 pts studied; 29 of 32 patients (90%) had typical clinical features (liver, peritoneal, omental, pelvic, mesenteric and/or retroperitoneal metastasis) and 18 of 32 (56%) had consistent IHC profiles (CK20+ and CDX2+). 29 pts (90%) received first-line (23 pts) and/or second-line (13 pts) colorectal cancer regimens. Objective response rates to first- and second-line therapies were 69% and 54%, respectively. The median, 2-, and 4-year survivals were 22 months, 43%, and 38%, respectively. Conclusions: Pts with CUP and a colorectal molecular profile diagnosis are responsive to colorectal chemotherapy regimens. When treated with site-specific therapy, these CUP pts have a median survival (22 months) similar to pts with known advanced colorectal carcinoma and superior to the survival of CUP pts receiving empiric chemotherapy (9 months). MTP can identify CUP pts with colorectal carcinoma and therapy with colorectal chemotherapy appears to improve their outcome.