The aim of the present study was to investigate the expression levels of the T-cell immunoglobulin and mucin domain-containing protein-3 (TIM-3) and galectin-9 proteins and their clinical value in esophageal squamous cell carcinoma (ESCC) in Chinese patients. The expression profiles of TIM-3 and galectin-9 in ESCC were determined by the immunohistochemical analysis of the postoperative pathological specimens of 45 patients with ESCC; a χ2 test was used to evaluate the association of TIM-3 and galectin-9 expression with clinicopathological parameters, in addition to univariate and multivariate Cox's proportional hazards model to analyze the prognostic value of the expression of TIM-3 and galectin-9 proteins. The proportion of samples exhibiting a high staining intensity for TIM-3 and galectin-9 were 22.22 and 15.56%, respectively: these samples were termed the TIM-3 high-expression group (HEG) and galectin-9-HEG. There was a negative correlation between the expression of TIM-3 and galectin-9 (R=-0.71, P<0.001). The results of Kaplan-Meier survival analysis led to the conclusion that, compared with the TIM-3 low expression group (LEG), patients in the TIM-3-HEG exhibited a poorer overall survival rate (χ2=6.049, P=0.0139). By contrast, patients in the galectin-9-HEG exhibited a significantly better overall survival rate than those in the galectin-9-LEG (χ2=4.915, P=0.0266). However, the levels of TIM-3 and galectin-9 expression were not identified as independent indicators for the prognosis of patients with ESCC. As high TIM-3 and low galectin-9 expression levels were associated with a poor prognosis for patients with ESCC in the present study, these proteins may be potential prognostic indicators for ESCC.