Traditional medicine has been used for a very long time, but scientific evidence regarding the therapeutic properties of traditional medicine has recently been required. Many components of herbs have been isolated, and their biological activities, evaluated. However, many of these herbs need to be biotransformed by bacteria in the large intestine in order to be biologically activated. The presence or absence of metabolically active bacteria in the large intestine is therefore important for biological activation. Inter-individual differences exist in the composition of human intestinal bacteria; biotransformation of traditional medicine outside the human body by using bacterial strains such as lactic acid bacteria (which are considered safe) has been used in an attempt to overcome such differences. This process yields what is referred to as fermented traditional medicine (FTM). FTMs have garnered attention for their enhanced biological activity compared to traditional medicine. Several studies using single herbs and formula support the availability of FTMs. However, the concrete concept of FTM is not yet established, and further discussions regarding the bacterial strains that have been used during fermentation and their safety are necessary. This report provides a general review and discussion of FTM with a view to promote better usage and safety in the future.