BACKGROUND The objective of this investigation was to define the phenotype and spatial distribution of Clara cells within the respiratory tract of common marmosets and to distinguish them from other non-ciliated cells (goblet cells, mixed type secretory cells). METHODS Non-ciliated cells were identified immunohistochemically using antibodies against Clara cell secretory protein and mucin 5AC. Transmission electron microscopy and scanning electron microscopy were performed to characterize Clara cells ultrastructurally. RESULTS Clara cells were present throughout the tracheobronchial tree, with lowest numbers in the trachea and highest numbers in bronchioles. Goblet cells and mixed type cells were scarce in the upper conducting airways and virtually absent within bronchioles. Ultrastructurally, Clara cells showed typical apical electron-dense granules and a prominent granular endoplasmatic reticulum. CONCLUSIONS Clara cells of common marmosets have species-specific morphological characteristics, which suggest grouping the common marmoset phenotypically between primates and rodents.