There are at least eight categories of cilia in the human body and malfunctioning of any one or several of them will have different consequences for the patient. A genetic error of the respiratory cilia (9 + 2) is the cause of the airways disease named immotile-cilia syndrome (or PCD), whereas defective ependymal cilia (9 + 2) carries an increased risk of hydrocephalus. When the so-called nodal cilia (9 + 0) of the early embryo are malfunctioning, there is a random determination of asymmetry of the heart and visceral organs (‘a 50% risk of situs inversus’). Some genes are responsible for the synthesis, transport, and assembly of the cilia, and mutations in these genes may lead to progressive degeneration of ciliary structures, such as the connecting cilium (9 + 0) of the photoreceptor cells—this is the cause of retinitis pigmentosa. Ciliary malfunctions due to genetic errors tend to be systemic and life-long, whereas acquired diseases are local and may be temporary only. Copyright © 2004 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.