This study investigated the mRNA levels of thymidylate synthetase (TYMS) and dihydropyrimidine dehydrogenase (DPYD) in esophageal squamous cell carcinoma (ESCC). TYMS and DPYD gene expression was quantified using real-time RT-PCR in 56 patients with ESCC, co-amplified with glyceraldehyde-3-phosphate dehydrogenase as an internal standard. The results were analyzed with reference to the clinicopathological characteristics and the prognosis of the ESCC patients. The TYMS and DPYD expression levels in patients positive with lymphatic invasion were significantly higher compared to those in patients who exhibited negative lymphatic invasion (TYMS P=0.0127, DPYD P=0.0127). Patients were classified into the groups high TYMS/DPYD, high TYMS but low DPYD, low TYMS but high DPYD and low TYMS/DPYD. The highest survival rate was found in the group with low TYMS/DPYD and the lowest survival rate in the group with high TYMS/DPYD (P=0.017). It was concluded that, on the basis of the multivariate analysis, TYMS mRNA expression is a candidate that serves as an independent prognostic factor for ESCC patients.