Multiciliated cells are characterized by coordinated arrays of motile cilia. In the respiratory tract, the maintenance of this array is essential to ensure proper ciliary and mucus clearance. The establishment and the maintenance of the ciliary set are mediated by the correct positioning of basal bodies at the cell cortex. While microtubule and actin cytoskeletons have been reported to regulate basal body lattices, an understanding of their detailed organization was missing until recently. Here, we describe how electron tomography can highlight the arrangement of the cytoskeletal networks and their interplay with basal bodies in ciliated cells in their tissular environment. Thanks to this approach, information in fine detail on large parts of the cell, dense in organelles, is provided. In combination with other approaches, such as transgenic animal models, electron tomography constitutes a powerful technique giving an overview of tissues and cells concomitantly with acquisition of three-dimensional detail.