Although natural medicines are generally considered to be safer than synthetic medicines, some reports on toxicity of many herb drugs, for example Traditional Chinese Medicine (TCM), attract more and more common public attention recently. The reasons for these cardiovascular toxic effects are not always satisfactory. Not all these clinical symptoms can be observed regularly. Cardiovascular toxicity concern is one of the hindrances for TCM to enter international markets. Therefore, we create web-based software for people to evaluate TCM cardiovascular toxicity. The software, TCM Cardiovascular Toxicity Prediction (TCMCardioTox), is based on structure similarity search algorithm (http://rcdd.sysu.edu.cn:8080/home.aspx). When a user enter a TCM name, the system interprets the name as a number of active component structures, and computes the structure similarities of the components against a number of known toxiphores. If one of the similarity is greater than a given similarity threshold, the TCM will be reported as an alert TCM for medical uses.