Although there are a few reports concerning the side effects and toxicity of herbal medicines, there has not yet been any report concerning their causes, mechanisms or prevention. We investigated the internal reports concerning the side effects and toxicity of herbal medicines. In the findings, liver disorder (hepatic injury) was found in 7 cases, kidney disorders (nephropathy) were found in 12 cases, heart disorders were found in 4 cases and mineral-caused diseases were found in 2 cases. Besides, we found the major cause of the side effects and toxicity was drug abuse, such as over-dosage and long term medication. So, we hope this report brings more attention to the safety and toxicity of herbal medicines.