The skull of the rare Malaysian snake Anomochilus leonardi is described in detail on the basis of a high-resolution X-ray computed tomographic scan of a mature specimen. Its skull anatomy is compared with that of Anomochilus weberi, as well as with that of scolecophidians and basal alethinophidians such as Anilius, Cylindrophis, uropeltines and selected Booidea. Anomochilus leonardi is found to be more paedomorphic than Anomochilus weberi. The genus Anomochilus most closely resembles uropeltines in skull anatomy. Both Anomochilus and uropeltines develop a ‘central rod design’ of skull morphology, which requires the presence of medial frontal pillars, in adaptation to burrowing habits. These pillars are an alethinophidian characteristic, absent in the skull of scolecophidians, which develop an ‘outer shell design’ in adaptation to burrowing. These results are discussed in the light of the hypothesis that scolecophidians and basal (i.e. non-macrostomatan) alethinophidians are ‘regressed macrostomatans’. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 671–685.