Background: The currently accepted definition of CTCs are cells that have: a nuclei, cytokeratin+ EpCAM+, and CD45-. Emerging evidence suggests that other rare circulating cells are present in the blood of metastatic cancer patients including CD45+ cytokeratin cells. A negative depletion process to isolate and quantify circulating tumor cells from the blood of head and neck cancer patients, using immunomagnetic separation was developed and currently be validated on a number of solid tumors, including SCCHN. Correlation of number of CTCs, tumor site, tumor stage, nodal status, smoking/alcohol abuse, histopathological characteristics, and clinical outcome was made. In addition, a subgroup of patients had blood collected immediately before and immediately after surgical resection to investigate any differences in the number of CTCs present. Methods: Prospective clinical follow-up study of 50 patients diagnosed with SCCHN undergoing surgical intervention had peripheral blood examined for the presence of CTCs. Five to 9 mL of peripheral blood was processed using previously described negative depletion enrichment with immunomagnetic tagging and removal of CD45 positive cells (Jatana et al. 2010). Subsequently, the cells were stained for cytokeratin. In addition, in some samples, other markers were targeted including vimentin, EGFR, and CD44. Results: With a mean follow-up of 24 months, data suggests that patients with detectable CTCs in the peripheral blood had a significantly reduced probability of disease-free survival (p=0.01). No correlation between the presence of CTCs with regard to tumor site, tumor stage, nodal status, smoking/alcohol use, and histopathological characteristics was observed. In a subgroup of 25 patients who had 2 consecutive samples taken immediately before and after resection, 64% of patients had an increase in number of CTCs after resection. We also identified a number of potential CTC, or cancer associated circulating cells of interest, including cells which are cytokeratin negative, vimentin positive and EGFR positive. Conclusions: Our initial data suggest a potential, important correlation between CTC and patient outcome and justifies further study.