Amplification of chromosomal region 11q13 is one of the genetic alterations most frequently observed in oral squamous cell carcinoma (OSCC). Both TAOS1, a recently identified gene, and EMS1 were thought as two important target oncogenes for driving 11q13 amplification, and their contributions to oral carcinogenesis were hypothesized. Therefore we investigated amplifications of TAOS1 and EMS1 genes and their relations to clinicopathological variables in premalignant lesions (leukoplakias) and primary OSCC. TAOS1 amplification, beginning from mild-dysplastic epithelia, occurred in 33.3% of leukoplakias and 51.5% of OSCC. EMS1 amplification, beginning from moderate-dysplastic epithelia, occurred in 20% of leukoplakias and 57.6% of OSCC. Both gene amplifications were significantly related to different stages of oral carcinogenesis (p<0.05). During multistage carcinogenesis, no gene amplification was observed in normal tissue and non-dysplastic leukoplakias while, in OSCC with metastasis, amplification frequency increased significantly (p<0.005). Both TAOS1 and EMS1 amplifications were significantly associated with larger tumor size, presence of lymph node metastasis, poor histological differentiation and advanced clinical stage. Our data suggested potential roles in oral carcinogenesis and that TAOS1 might be involved earlier than EMS1. Both genes might be candidate biomarkers for diagnosis and prognosis in OSCC.