Ciliated cells of the respiratory epithelium play an essential role in the mechanisms of mucociliary clearance, and ultrastructural alterations of cilia are known to be associated with respiratory disease. The aim of this study was to evaluate the presence of ciliary changes in common marmosets (Callithrix jacchus) of different age groups and to compare healthy animals with animals suffering from subclinical chronic inflammatory pulmonary lesions. Therefore, samples of different sites of the tracheobronchial tree from 24 common marmosets were investigated by transmission electron microscopy. Ciliary alterations were present in all animals and were represented by compound cilia ("bulging/adhesive type"), extramatrix, extratubuli, and disorientation of the microtubular arrangement. Ciliary alterations affected less than 1% of cilia (average 0.06%-0.55%) with no statistically significant differences between age groups, sample localizations, or healthy and sick animals. The study results suggest that ciliary alterations of secondary nature are a common background finding in common marmosets with individual variability in abundance and have to be considered when interpreting ultrastructural data from respiratory studies.