Side population (SP) cells are isolated from various tissues and cell lines based on the exclusion of DNA-binding dye Hoechst 33,342 and exhibit potent stem cell characteristics. There have been few previous reports of SP cells in head and neck cancer cell lines. Thus, we isolated SP cells from oral squamous cell carcinoma cell line, Ho-1-N-1. Ho-1-N-1 contained 3.0% SP cells. Ho-1-N-1 SP cells showed self-renewal capacity, generating both SP and non-SP cells. Next, we analyzed differentially expressed genes between Ho-1-N-1 SP and non-SP cells using GeneChip microarray and quantitative real-time RT-PCR. SP cells expressed high levels of ATP-binding cassette transporters with related multidrug resistance (MDR) genes. The expression of ABCB1 and ABCG2 were significantly up-regulated in Ho-1-N-1 SP cells. In addition, the expression of CFLAR, BCL2 and BCL2A1 which are associated with anti-apoptosis, were also significantly increased in the SP cells. Chemoresistance to anticancer agents, including 5-fluorouracil and carboplatin, were compared between Ho1-N-1 SP and non-SP cells using flow cytometry and tetrazolium salt microtiter plate assay. Ho-1-N-1 SP cells survived significantly longer and SP ratio remarkably increased after anticancer agent treatment compared to non-SP cells. Immunocytochemical staining and apoptosis assay validated these results, and suggested an anti-apoptotic potential for Ho-1-N-1 SP cells. Ho-1-N-1 SP cells survived with various agents which were not only probably due to high level expression of ABC transporters, but also anti-apoptotic proteins. These observations indicated that Ho-1-N-1 SP cells were MDR phenotype and should be the main target for effective cancer therapy.