The cranial anatomy of the Lower Jurassic ornithischian dinosaur Heterodontosaurus tucki Crompton & Charig, 1962 is described in detail for the first time on the basis of two principal specimens: the holotype (SAM‐PK‐K337) and referred skull (SAM‐PK‐K1332). In addition several other specimens that have a bearing on the interpretation of the anatomy and biology of Heterodontosaurus are described. The skull and lower jaw of Heterodontosaurus are compact and robust but perhaps most notable for the heterodont dentition that merited the generic name. Details of the cranial anatomy are revealed and show that the skull is unexpectedly specialized in such an early representative of the Ornithischia, including: the closely packed, hypsodont crowns and ‘warping’ of the occlusal surfaces (created by progressive variation in the angulation of wear on successive crowns) seen in the cheek dentition; the unusual sutural relationships between the bones along the dorsal edge of the lower jaw; the very narrow, deeply vaulted palate and associated structures on the side wall of the braincase; and the indications of cranial pneumatism (more commonly seen in basal archosaurs and saurischian dinosaurs). Evidence for tooth replacement (which has long been recognized, despite frequent statements to the contrary) is suggestive of an episodic, rather than continuous, style of tooth replacement that is, yet again, unusual in diapsids generally and particularly so amongst ornithischian dinosaurs. Cranial musculature has been reconstructed and seems to conform to that typically seen in diapsids, with the exception of the encroachment of M. adductor mandibulae externus superficialis across the lateral surface of the temporal region and external surface of the lower jaw. Indications, taken from the unusual shape of the occlusal surfaces of the cheek dentition and jaw musculature, are suggestive of a novel form of jaw action in this dinosaur. The taxonomy of currently known late Karoo‐aged heterodontosaurids from southern Africa is reviewed. Although complicated by the inadequate nature of much of the known material, it is concluded that two taxa may be readily recognized: H. tucki and Abrictosaurus consors. At least one additional taxon is recognized within the taxa presently named Lanasaurus and Lycorhinus; however, both remain taxonomically problematic and their status needs to be further tested and may only be resolved by future discoveries. The only other named taxon, Geranosaurus atavus, represents an invalid name. The recognition of at least four distinct taxa indicates that the heterodontosaurids were speciose within the late Karoo ecosystem. The systematics of Heterodontosaurus and its congeners has been analysed, using a restricted sample of taxa. A basal (nongenasaurian) position within Ornithischia is re‐affirmed. There are at least four competing hypotheses concerning the phylogenetic placement of the Heterodontosauridae, so the evidence in support of the various hypotheses is reviewed in some detail. At present the best‐supported hypothesis is the one which places Heterodontosauridae in a basal (non‐genasaurian) position; however, the evidence is not fully conclusive and further information is still needed in respect of the anatomy of proximate outgroups, as well as more complete anatomical details for other heterodontosaurids. Heterodontosaurids were not such rare components of the late Karoo ecosystem as previously thought; evidence also suggests that from a phylogenetic perspective they occupied a potentially crucial position during the earliest phases of ornithischian dinosaur evolution. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011.