Background: Immunotherapy is one of the most promising therapeutics for hepatocellular carcinoma (HCC), and the immune infiltration status in tumors could be used as a biomarker for immunotherapy. However, evaluation of immune infiltration is usually based on RNA-Seq (transcriptome sequencing), which is limited in clinical practice due to the difficulty of handling RNA. On the other hand, WES (whole exome sequencing) is frequently performed to detect tumor mutations in cancer clinic. Therefore, we try to compare T cell infiltration in hepatocellular carcinoma obtained from WES data and RNA-Seq data, evaluate the potential of T cell infiltration from WES data as a biomarker for immunotherapy. Besides, we also evaluated the association of T cell fraction obtained from WES data and other clinical information. Methods: Seventy pairs of HCC tumor and matched normal tissue samples underwent both WES and RNA-Seq. T cell ExTRECT score and mcpCounter score were used to represent the immune infiltration status, and they were generated from WES data and RNA-Seq data respectively. Tumor mutational burden (TMB) score and some characteristics (tumor size, blood pressure, etc.) were also calculated for correlation analysis. Results: T cell ExTRECT score was positively correlated with mcpCounter score (Spearman correlation coefficient: 0.54). While TMB score showed no correlation with T cell ExTRECT score (Spearman correlation coefficient: -0.06) and mcpCounter score (Spearman correlation coefficient: -0.09). Besides, T cell ExTRECT score was negatively associated with main tumor size (Spearman correlation coefficient: -0.38) and High Blood Pressure (Spearman correlation coefficient: -0.37). Conclusions: These results suggest that T cell ExTRECT score obtained from WES and mcpCounter score generated by RNA-seq data is highly correlated, and neither of them is associated with TMB score. T cell ExTRECT score could be used to evaluate immune infiltration in hepatocellular carcinoma, and may serve as a biomarker for immunotherapy regardless of TMB score. Further investigation is still needed to evaluate the clinical outcome of immunotherapy for hepatocellular carcinoma with T cell ExTRECT score.