Herbal medicine has long been viewed as a valuable asset for potential new drug discovery while herbal ingredients’ metabolites, especially the in vivo metabolites were often found to gain better pharmacological, pharmacokinetic and even better safety profiles compared to their parent compounds. However, these herbal metabolite information is still scattered and waiting to be collected. Although the metabolites are hard to obtain because of the low-content and complicated lab procedures, HIM database manually collected almost all the available in vivo metabolism information for herbal active ingredients, as well as their corresponding bioactivity, organs and/or tissues distribution, toxicity, ADME and the clinical research profile when possible. Currently HIM contains 361 ingredients and 1104 corresponding in vivo metabolites from 673 reputable herbs. Tools of structural similarity, substructure search and Lipinski’s Rule of Five are also provided. Various links were made to PubChem, PubMed, TCM-ID (Traditional Chinese Medicine Information database) and HIT (Herbal ingredients’ targets databases).