Multiciliated cells (MCCs) on Xenopus embryo skin are popular model system to study the process of cilia formation and the function of genes involved in ciliopathy, a human diseases caused by cilia dysfunction. However, proteins comprising the cilia structure in Xenopus MCCs are not directly investigated so far. In this study, using improved cilia isolation method for label-free shotgun proteomics, we identified over 2,000 proteins from almost intact cilia structure isolated from Xenopus mucociliary epithelia.