Cape Verde has a higher number of reptile taxa and endemics than any of the five archipelagos in the Macaronesian region. Mapping the precise distributions and assessing the conservation status of reptiles is the first step towards effective conservation. Presence/absence and abundance data were gathered from extensive fieldwork and post-1980 literature. Evaluation of conservation status was considered at specific and subspecific levels, following IUCN Red List criteria and using RAMAS. Fieldwork confirmed the occurrence of 34 of 37 previously recorded taxa (31 native, three exotic). One taxon continues to be considered Extinct. Three broad distribution and rarity patterns were identified: widespread and abundant taxa occurring on ≥ 2 islands/islets, widespread or abundant taxa restricted to one island, and rare or limited range taxa occurring on small areas of islands or islets. More than a third of taxa have areas of occupancy < 20 km2 and extents of occurrence < 100 km2. Geckos are rarer than skinks because of their high habitat specialization, with 58% occurring on only one island/islet. About half of all taxa are potentially threatened, twice the proportion of those in the Canary Islands, a difference that could be explained by the smaller area and greater aridity of the Cape Verde islands. The criterion used for most threat categorizations is geographical range, and the most pervasive threats are natural disasters, intrinsic factors of the species and introduced species. The importance of applying conservation status at the subspecific level to island endemics is emphasized. Several conservation measures are proposed, including optimized design of protected areas.