Alopecia, that is, lack of hair in any quantity, is a frequent complaint of pet owners. Although mostly acquired, rare congenital forms of alopecia exist that are associated with abnormalities in hair follicle morphogenesis. Congenital alopecias can result in changes in quality or quantity of hair follicles and the hair fibres produced by them. They vary in terms of clinical presentation and mode of inheritance. Histopathology is usually needed in order to differentiate between a reduced number of otherwise normal hair follicles and qualitative hair follicle abnormalities. Although our understanding of the molecular mechanisms that drive hair follicle morphogenesis in mice and humans has significantly increased during the last decade, still very little is known about congenital alopecias in domestic animals. Because of their rarity and the general lack of knowledge about their pathophysiology, classification of congenital alopecias in domestic animals is still unsatisfactory. This article reviews hair follicle morphogenesis and its most important molecular mechanisms, and it discusses the various forms of congenital alopecia occurring in domestic animals that have been described in the literature, differentiating between hair follicle aplasia, hair follicle dysplasia (i.e. defects associated with hair follicle development and defects associated with hair shaft formation), and neuroectodermal dysplasias, the latter involving the hair follicle pigmentary system.