An increasing number of reports have demonstrated the presence of tumor-specific DNA in cancer patients' plasma/serum. These findings offer the prospective of serologic tumor markers that may aide in early disease detection, predict subclinical disease progression, and monitor treatment responses. However, for patients with colorectal cancer (CRC), there are few reports using this approach, with most revealing poor sensitivity. In contrast to tumors of other organ systems, CRCs drain predominantly via the mesenteric/portal veins (MV) to the liver. We hypothesize that because of this unique relation, tumor DNA may be less abundant in CRC patients' systemic circulation as compared to the mesenteric/portal system. At the time of surgery, paired blood was collected from both the peripheral vein (PV) and MV from 33 CRC patients. DNA was isolated from serum, quantified and assessed for loss of heterozygosity (LOH) using a panel of 11 microsatellite markers corresponding to regions on six chromosomes frequent for LOH in CRC. In addition, 16 samples were assessed for the presence of hypermethylated DNA for tumor suppressor genes: MGMT, P16, RAR-beta2, RASSF1A, and APC. Circulating tumor DNA associated with LOH or methylation was more frequently detected in the MV of patients, 11 (33%) and 6 (38%), as compared to PV, 9 (27%) and 1 (6%), respectively. This study is the first to identify the presence of increased tumor DNA in the direct efferent venous drainage system of CRC and its variation as compared to systemic circulation. The findings provide important evidence supporting the origin of tumor-associated DNA in circulation, which merits consideration when devising blood-based nucleic acid assays for the assessment of CRC.