Antrodia cinnamomea is an expensive and highly valued folk medicinal fungus that grows only inside the rotten trunk of Cinnamomum kanehirae, an evergreen broad-leaved tree. This fungus has recently been used commercially in the formulation of nutraceuticals and functional foods in Taiwan. It has been used for centuries as a detoxificant in cases of food poisoning, diarrhea, vomiting, hepatic disease and various kinds of cancers. The present study investigated the effects of Antrodia cinnamomea on mutagenicity using a bacterial reverse mutation assay employing the Salmonella typhimurium strains TA97, TA98, TA100, TA102, and TA1535. The effects of Antrodia cinnamomea on chromosome structure were tested in Chinese hamster ovary (CHO) cells. Antrodia cinnamomea was not mutagenic in all bacterial strains and it was not genotoxic in CHO cells.