Problem Head and neck squamous cell cancer (HNSCC) is a heterogeneous cancer that continues to pose major clinical problems. Much recent attention has been given to the concept that cancers contain a relatively small population of stem-like cells (CSCs) that are able to regrow the full complexity of the tumor upon transplantation into an experimental animal. Furthermore, there is growing evidence that these stem cell-like populations may be an important factor in disease progression and resistance to current treatments. Background Establishing that stem cells are present in HNSCC, and contribute to treatment resistance in these cancers, provides the rationale for this gene expression study. Finding genes that are commonly differentially present in stem cells will provide the basis for future biomarkers that can help to improve patient management through better prognostic information and selection of the most appropriate treatment modalities and scheduling. Hypothesis The hypothesis of the study is that there are common genes over or underexpressed specifically in stem cell populations in HNSCC. Research. A panel of five (UT14 UT16A, UT24A, UT30 and UT33) low passage HNSCC cancer lines was studied. CSC (and non CSC) were isolated from these cell lines by high-speed cell sorting using two different flow cytometry techniques 1) Hoechst 33342 “side” population and 2) the Aldefluor assay. RNA was extracted from the sorted populations for gene expression analysis. Differentially expressed genes were determined by utilizing Affymetrix Human Exon 1.0 ST microarrays and subsequent analysis in Partek’s Genomics Suite. Sorted cells CSCs and non-CSCs were studied radiosensitivity using clonogenic survival assays. Observations The two methods of isolation identified different proportions of “stem” cells. The “side” population was less prevalent and ranged from 0.3 to 3.7% in the 5 cell lines whereas Aldefluor positive cells ranged from 6 to 31.4%. Only UT33 had a similar proportion of cells (3.7 vs 6%) by the two methods. In the analysis so far using ANOVA with a significance of p≤0.05 and a fold-change cutoff of 1.5, 83 differentially expressed genes were identified by comparing “side” population to non-“side” population samples. Of the 45 genes that were up-regulated, 22 were associated with histones. Stem cells, identified by the “side” population, show increased radioresistance compared to non-CSCs. Conclusions The high incidence of histone gene overexpression in “side” population cells is consistent with the known involvement of chromatin packaging in the maintenance of the stem cell phenotype and the involvement of histones in DNA repair may relate to the increased radioresistance of stem cells. Further studies on the epigenetic regulation of histones in stem cells may provide future avenues for therapeutic targets to be used in conjunction with chemoradiation.