OBJECTIVE: Recent studies have revealed that the ability of cancer cells to undergo intermediate state of EMT, partial EMT (p-EMT) poses a higher metastatic risk rather than complete EMT. Here we examined the prognostic value of p-EMT-related genes in head and neck squamous cell carcinoma (HNSCC) by bioinformatic approaches. MATERIALS AND METHODS: We used RNA-seq data of 519 primary HNSCC cases obtained from TCGA database. We compared the expression of p-EMT-related genes in HNSCC tissues with normal tissues. We evaluated the prognostic value of p-EMT-related genes in HNSCC cases by Log-rank test. We examined the expression of p-EMT-, EMT-, and epithelial differentiation-related genes by qPCR. RESULTS: Among p-EMT-related genes that were highly expressed in HNSCC cases, high expression of SERPINE1, ITGA5, TGFBI, P4HA2, CDH13, and LAMC2 was significantly correlated with poor survival of HNSCC patients. By gene expression pattern, HNSCC cell lines were classified into three groups; epithelial phenotype, EMT-phenotype, and p-EMT phenotype. CONCLUSIONS: Our findings suggest that p-EMT program may be involved in poor prognosis of HNSCC. SERPINE1, ITGA5, TGFBI, P4HA2, CDH13, and LAMC2 can be used for a prognostic marker. Moreover, HNSCC cells with p-EMT phenotype can be a useful model for investigating a nature of p-EMT.