This paper presents the synthesis of the research project titled “Phonological comparison of Muisca with Uwa, Barí and Nasa Yuwe”. This work involved a comparative exercise based on the phoneme inventories of the four above-mentioned languages, and a list of glosses compiled from previous studies. Some principles of the comparative method were considered in order to, firstly, evaluate the likely correlation between geographical proximity of the territories where the languages compared are spoken, and their cognation rates; secondly, verify punctually the cognation rates between Muisca and Nasa Yuwe, a language which has been considered as probably related to the Chibchan family; thirdly, analyze the sources to apply the comparative method to Colombian native languages; and, finally, determine limitations when applying this method. Conclusions present cognation rates among the languages analyzed, all of which yielded higher rates in the comparison Uwa-Muisca, and were lower in the comparisons Barí-Muisca and Nasa Yuwe-Muisca, respectively. Furthermore, the Protochibchan change tendencies towards attested forms in the languages observed were also described.