Herbal medicines are increasingly used to treat various diseases and lots of studies have been reported that they had benefits in treating and preventing of diseases. But organic toxicity is increasingly recognized as herbal medicines become more popular in industrialized countries. Some herbal products potentially benefit people with lots of diseases, however these benefits remain generally unproved in humans, and a greater awareness for potential adverse effects is required. A herb containing a wide variety of, mostly unknown, substances may well include some with unwanted effects. This review focuses on emerging organic toxicities that have been observed associated with various herbal preparations involving the liver, kidney, and heart, and patterns of organ injury, potential risk factors for organic toxicities. In addition to the potential for organic toxicities, drug drug interactions between herbal medicines and conventional agents may affect the efficacy and safety of concurrent medical therapy. Appropriate reporting and regulatory system to monitor herbal toxicity are required, in conjunction with ongoing scientific evaluation of the potential benefits of phytotherapy.