PURPOSE: The apolipoprotein E (APOE) gene is one of the strongest genetic determinants of the risk of developing late-onset Alzheimer's disease (AD) and may also increase the risk of cancer. However, its importance goes far beyond this. The aim of this study was to comprehensively analyze the potential role and prognostic value of APOE in hepatocellular carcinoma (HCC) using bioinformatics and multiplex fluorescence immunohistochemistry (mIHC). METHODS: Clinicopathologic samples from 90 hCC patients enrolled between April 2007 and June 2012 were included in this study. Researchers used tissue microarrays (HLiv180Su09) and multiple fluorescent immunohistochemical analyses to validate APOE protein expression and patient prognosis. Several online databases were used to investigate APOE expression and prognosis in HCC, followed by a comprehensive analysis of correlations between APOE and clinicopathologic features, immune cell infiltration levels, immune checkpoint genes, mutations, and functional enrichment analysis. The distribution of APOE in immune cell populations was also determined using a single-cell database. RESULTS: APOE mRNA was significantly overexpressed in HCC at both transcriptional and translational levels. Survival analysis suggested that APOE might be a favorable prognostic indicator for HCC patients. In addition to its involvement in immune cell infiltration, immune checkpoint gene expression, genetic variation, immunomodulatory genes, and methylation alterations in HCC, enrichment analysis showed that APOE was involved in multiple cancer-related signaling pathways. CONCLUSION: This study comprehensively examines the critical role of APOE in HCC and highlights its significant potential as a biomarker and therapeutic target. This finding not only paves the way for new avenues of research in HCC, but also provides valuable insights into clinical diagnosis and treatment strategies.