It has been found that natural microorganism have a siginificant role in the production and development of new medicines. The present study aimed to evaluat biotransformation of atropine, 4-hydroxy coumarin, 8-hydroxy quinoline, indole and industrially compound (penicillin G), arrive in the human body, by some natural microorganism (Escherichia coli ATCC 25922, Bacillus subtilis ATCC 6051, Lactobacillus acidophilus ATCC 314, Mycobacterium Bovis (BCG), Saccharomyces cerevisiae ATCC 5052, and Candida albicans ATCC 10231), for the first time. The best values for the concentration and required times were evaluated for each metabolites in microbioal biotransformation process. The progress of the formation of the metabolites were monitored by Thin Layer Chromatography (TLC) method. Obtained results showed that only indole, atropine, and 4-hydroxy coumarin could be biotransformed by Candida albicans ATCC 10231, Escherichia coli ATCC 25922, and Saccharomyces cerevisiae ATCC 5052, respectively.