The therapeutic effects of the plant species used in homeopathy have never been subjected to systematic analysis. A survey of the various Materiae Medicae shows that over 800 plant species are the source of medicines in homeopathy. As these medicines are considered related to one another with respect to their therapeutic effects for treating similar symptoms, the aim is to classify and map them using the concept of homology. This involves placing the discipline of homeopathy into a comparative framework using these plant medicines as taxa, therapeutic effects as characters, and contemporary cladistic techniques to analyse these relationships. The results are compared using cladograms based on different data sets used in biology (e.g. morphological characters and DNA sequences) to test whether similar cladistic patterns exist among these medicines. By classifying the therapeutic actions, genuine homologies can be distinguished from homoplasies. As this is a comparative study it has been necessary first to update the existing nomenclature of the plant species in the homeopathic literature in line with the current International Code of Botanical Nomenclature.