5-Fluorouracil (5-FU) has been used for oral squamous cell carcinoma (OSCC) treatments, and the acquisition of resistance is the major problem to successful OSCC treatment. It has been reported that the epithelial to mesenchymal transition (EMT) is associated with chemoresistance in several types of cancers. In the present study, we established 5-FU-resistant OSCC cell lines (HSC2/FU and HSC4/FU), and aimed to elucidate the mechanism(s) involved in resistance in association with its EMT characteristics. MTT assay revealed that HSC2/FU is about 14-fold more resistant compared to HSC2, and HSC4/FU is 5-fold more resistant compared to HSC4. TUNEL assay also showed a dramatically decreased number of apoptotic cells in the 5-FU-resistant OSCC cell lines compared to each parental cell after treatment with 5-FU. Moreover, the 5-FU-resistant OSCC cell lines had typical morphologic phenotypes of EMT; loss of cell-cell adhesion, increased formation of pseudopodia and spindle-shaped morphology. Western blot analysis showed downregulated E-cadherin, and upregulated N-cadherin and Twist in the 5-FU-resistant OSCC cell lines. Results of our tumor xenograft studies coincide with our in vitro study data that confirmed the 5-FU resistant nature of HSC2/FU and HSC4/FU tumors. Moreover, immunohistochemistry showed that EMT changes (downregulated E-cadherin, and upregulated Twist and N-cadherin) occurred in the 5-FU-resistant xenografted tumor cells. These results suggest that EMT has important roles in the 5-FU-resistant OSCC cells, and that these resistant cells may be considered as useful tools for understanding the mechanisms involved in 5-FU resistance in OSCC.