Introduction: Recent work indicates the there is a small subpopulation of malignant stem cells that are responsible for the initiation, growth, recurrence and metastasis of solid tumors, including squamous cell carcinoma of the head and neck region (HNSCC). Cells with stem cell characteristics have also been identified in cell lines derived from other cancers. The aim of the present work was to characterize stem cell markers in HNSCC cell lines. Methods: The ATCC SCC 9, 15, and 25 established cell lines were examined for their pattern of colony morphologies, expression of the putative stem cell markers CD44, CD133 and CD29 by FACS analysis and their ability to form spheroids in the absence of attachments. To determine the relationship of CD44 expression to cisplatin sensitivity in vitro, two stable CD44 expressing clones were created in the established ATCC SCC25 cell line and were analyzed for cisplatin sensitivity. Results: All HNSCC established cell lines showed a holoclone/meroclone/paraclone series of colony morphologies and formed spheres when cultured in suspension. Re-passaging of primary spheres of all cell lines showed the ability to form secondary spheres with an increase in the total number of spheres. When cells from secondary spheres were dissociated and plated into standard tissue culture plates, they adhered and formed colonies with mainly holoclone morphologies. FACS analysis of the primary \#8216;cancer spheroids\#8217; showed a co-expression of high levels of CD44 and CD29, but only a very small fraction of highly expressing CD133 showed high co-expression of CD44 or CD29. The average IC50 (drug dose to inhibit 50% of cell growth) for the HNSCC cell line with no expression of CD44 was Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 4902.