Similar to Unani (Greek) medicine, Iranian traditional medicine is based upon the theory of humors of the body. Thus, it is obvious that the quality of development of different body organs have originated from this theory. According to the Iranian traditional medicine, body organs have developed from humors, and humors in turn have originated from food. The condition of the development of different organs and also the relationships among the organs are the noteworthy points in the Iranian traditional medicine. In the Iranian traditional medicine, the body organs are classified with various methods according to their origin, function, and their relationship with other organs. We have presented the classifications in details. The analysis of relationships among organs, faculties, spirits, and their resulted activities is surprisingly so robust and diagrammatic, such that the rules are adhered in all sections. The Iranian traditional medicine is different from Galen’s teachings from this viewpoint. In our traditional medicine system, the faculties and spirits are known to have materialistic quality, since they originate from cardinal organs, and their transportation is done through veins, arteries, and nerves. As veins transports natural and animal spirits (in trivial amounts) besides transporting humors, their role is of greater importance in this system.