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As a complex disease, the development and progression of hepatocellular carcinoma (HCC) involves the interactions of multiple proteins, genes and miRNAs in various biological pathways, and it has been extensively studied with different high-throughput techniques. However, efforts to integrate multiple data sources at different levels, especially with regard to biological pathways and interaction networks, are still negligible in the HCC research field. We have built a database of the HCC network (HCCNet) by integrating interactions of multiple proteins, genes and miRNAs in biological pathways, and manually collecting all of the HCC-related genes and miRNAs from the literature in combination with a bioinformatic analysis of the collected HCC expression data (Supplementary information, Data S1). Currently, there are 37 811 experimentally confirmed protein-protein interactions (PPIs), 9 148 experimentally confirmed transcriptional regulatory interactions (TRIs), 114 miRNA-target gene interactions, 2 234 high-confidence HCC-related genes and 160 HCC-related miRNAs available in the database. The database also provides an online graphic analysis tool to view the interactions among HCC-related proteins, genes and miRNAs. HCCNet is a helpful platform to explore the molecular mechanisms that underlie human HCC. The database can be accessed at http://www.megabionet.org/hcc.