An algorithm is described for the functional and morphological analysis of the trachea in small laboratory animals, including the consecutive in vivo study of the velocity of mucus movement and in vitro analysis of motor activity of the ciliary apparatus in combination with the histological study of the organ. The proposed methodological approaches permits, during a short period of time (20-30 min per one animal) to supravitally register and document in digital format video files with their subsequent visual estimation and mathematical analysis of the parameters studied. These techniques provide high reproducibility of the results with a maximum efficiency and information value and permit to undertake a comprehensive morpho-functional analysis of the investigated object.