ChemDIS is a chemical-disease inference system based on chemical-protein interactions. By integrating the chemical-protein interactions and protein-disease interactions, the diseases associated with a given chemical can be inferred from the chemical-protein-disease relatioinship. ChemDIS provides enrichment analysis tools for identifying chemical-associated Gene Ontology (GO), pathway (KEGG, Reactome and SMPDB) and Disease Ontology (DO and DOLite) based on a hypergeometric distribution. The chemical-protein interactions in humans were retrieved from STITCH database v5.0 and v4.0. ChemDIS is expected to be a useful chemical-disease inference system for assessing potential risks associated with enviromental chemicals. Our previous study on maleic acid provides a case study of chemical-protein-disease inference (Lin et al., 2014). ChemDIS also serves as a hypothesis generation tool for experimental validation. For example, the effects of maleic acid on calcium levels and neuronal systems have been identified based on ChemDIS and experimentally validated (Wang et al., 2017).