Chlamiophila pneumoniae were detected in targeted sections of mouse lung tissue by means of transmission electron microscopy and immunofluorescent staining. Incorporation of microorganisms into the axonemal matrix of cilia was observed 24 h after infection. The ciliary axoneme was characterized by pronounced swelling. At the late stages Chlamiophila pneumoniae were present in cytoplasmic vacuoles. Structural abnormalities and dysfunction of mucociliary clearance followed by incorporation of Chlamiophila pneumoniae into the cytoplasm of epitheliocytes were revealed in the early stage of infection. The proposed method allows studying the very early events of Chlamiophila pneumoniae infection.