A precise knowledge of the spatial distribution of taxa is essential for decision-making processes in land management and biodiversity conservation, both for present and under future global change scenarios. This is a key base for several scientific disciplines (e.g. macro-ecology, biogeography, evolutionary biology, spatial planning, or environmental impact assessment) that rely on species distribution maps. An atlas summarizing the distribution of European amphibians and reptiles with high quality maps was published 17 years ago by the Societas Europaea Herpetologica (SEH). Since then, more accurate data became available for many areas, while taxonomic changes also took place. The lack of an updated atlas of European amphibians and reptiles is widely acknowledged by the SEH community, and this need has been one of the main driving forces for the present effort. Compiling and standardising data on the distribution of European amphibian and reptile species at the European scale is a fundamental step. Here we present an updated dataset of all European amphibian and reptile species at 50×50 km UTM cells resolution, together with preliminary species distribution maps. The information was compiled from different sources of data: published books and websites, ongoing national atlases, personal data provided to the SEH, the 1997 European Atlas, and the Global Biodiversity Information Facility. The resulting database comprises more than 384,000 grid and locality records distributed across 40 countries. We calculated species richness maps as well as maps of Corrected Weighted Endemism, and defined species distribution types by hierarchical cluster analysis using Jaccard’s index as association measure. Preliminary maps for all European amphibian and reptile species are made available open-access on the journal webpage of Amphibia-Reptilia, including GIS-shapefiles for free use. We expect this work to be a preliminary step towards an interactive, dynamic and online distributed database system (NA2RE system) of the current spatial distribution of European amphibians and reptiles.