Cilia are highly conserved organelles with diverse motility and sensory functions. They project from most eukaryotic cells and are almost always found in vertebrates. Recent research in the field has brought the importance of cilia function to the forefront by identifying crucial roles for cilia in signaling pathways and maintenance of cellular homeostasis. Motile cilia are important for fluid and particle movement over epithelial surfaces, and for vertebrate sperm and unicellular algae motility. Primary (immotile) cilia are involved in mechanic and chemical sensing on almost all cells of our body. They are critical in signal transduction pathways regulating intracellular Ca2+ levels, as well as in the Hedgehog planar cell polarity and autophagy pathways. Defects in cilia development and function have significant effects on the development of the body and functioning of the various organs, leading to complex human genetic diseases, collectively known as ciliopathies. Due to the explosion of molecular-based research on cilia, the methods used to study ciliary structure and function are getting more and more importance. This Methods Collection is dedicated to strategies and techniques employed for deciphering the underlying mechanisms of ciliary structure, function, and intraflagellar transport. This section will provide methods ranging from ciliary immunohistochemistry and visualization of ciliary motility, to functional characterization of primary cilia that will aid in providing new insights into developmental and disease phenotypes.