Cilia are organelles present on almost every cell within the body. In the respiratory tract, motile cilia line the epithelial surface and beat in a coordinated fashion to clear mucus from the airways. Mucociliary dysfunction is implicated in a number of lung diseases including cystic fibrosis, chronic obstructive pulmonary disease, bronchiectasis and primary ciliary dyskinesia. Recent microscopy advances such as electron tomography have developed our understanding of the structure and function of these important organelles. In this review we discuss electron tomography and its relevance to respiratory cilia.