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From the earliest records regarding the use of medicinals to today, the toxicity of certain substances has been described in all Chinese materiae medicae. Since TCM has become more popular in the Western world, there are increasing concerns about the potential toxicity of many traditional Chinese medicinals including plants, animal parts and minerals. Traditional Chinese herbal remedies are conveniently available from grocery stores in most Chinese neighborhoods; some of these items may contain toxic ingredients, are imported into the U.S. illegally, and are associated with claims of therapeutic benefit without evidence. For most medicinals, efficacy and toxicity testing are based on traditional knowledge rather than laboratory analysis. The toxicity in some cases could be confirmed by modern research (i.e., in scorpion); in some cases it couldn't (i.e., in Curculigo). Traditional herbal medicines can contain extremely toxic chemicals and heavy metals, and naturally occurring toxins, which can cause illness, exacerbate pre-existing poor health or result in death. Botanical misidentification of plants can cause toxic reactions in humans. The description on some plants used in traditional Chinese medicine have changed, leading to unintended intoxication of the wrong plants. A concern is also contaminated herbal medicines with microorganisms and fungal toxins, including aflatoxin. Traditional herbal medicines are sometimes contaminated with toxic heavy metals, including lead, arsenic, mercury and cadmium, which inflict serious health risks to consumers. Also, adulteration of some herbal medicine preparations with conventional drugs which may cause serious adverse effects, such as corticosteroids, phenylbutazone, phenytoin, and glibenclamide, has been reported.

Substances known to be potentially dangerous include Aconitum, secretions from the Asiatic toad, powdered centipede, the Chinese beetle (Mylabris phalerata), certain fungi, Aristolochia, Arsenic sulfide (Realgar), mercury sulfide, and cinnabar. Asbestos ore (Actinolite, Yang Qi Shi, 阳起石) is used to treat impotence in TCM. Due to galena's (litharge, lead(II) oxide) high lead content, it is known to be toxic. Lead, mercury, arsenic, copper, cadmium, and thallium have been detected in TCM products sold in the U.S. and China.

To avoid its toxic adverse effects Xanthium sibiricum must be processed. Hepatotoxicity has been reported with products containing Polygonum multiflorum, glycyrrhizin, Senecio and Symphytum. The herbs indicated as being hepatotoxic included Dictamnus dasycarpus, Astragalus membranaceous, and Paeonia lactiflora. Contrary to popular belief, Ganoderma lucidum mushroom extract, as an adjuvant for cancer immunotherapy, appears to have the potential for toxicity. A 2013 review suggested that although the antimalarial herb Artemisia annua may not cause hepatotoxicity, haematotoxicity, or hyperlipidemia, it should be used cautiously during pregnancy due to a potential risk of embryotoxicity at a high dose.

However, many adverse reactions are due to misuse or abuse of Chinese medicine. For example, the misuse of the dietary supplement Ephedra (containing ephedrine) can lead to adverse events including gastrointestinal problems as well as sudden death from cardiomyopathy. Products adulterated with pharmaceuticals for weight loss or erectile dysfunction are one of the main concerns. Chinese herbal medicine has been a major cause of acute liver failure in China.

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