In this paper we present a unique spatial dataset of Neandertal sites in Europe. Information on topographic locations with human fossils was collected in the course of our own work and from a comprehensive literature review. The fossils are classified into Pre-Neandertals, Early Neandertals and Classic Neandertals. Based on this dataset, we explored the environmentally constrained site-selection criteria of Neandertals. The site locations are described by topographic indices giving information on climatic, strategic and water-related criteria on which Neandertals may have based their site selection. We applied two different explorative statistical approaches for the three Neandertal fossil classes, deriving robust and consistent results for Early and Classic Neandertals. However, because of the nature and size of the response variables showing a certain heterogeneity and due to landscape dynamics, which might have occurred in the observed periods, we focus on the overall trends that the data show. The study reveals that Early and Classic Neandertals not only show specific spatial distributions but are also characterized by different environmental preferences. Both models reproduce the particular site preferences for Early and Classic Neandertals, which demonstrate a higher relevance of climatic issues for the Early Neandertals and a pronounced strategic component for the Classic Neandertals. Additionally, the methodology allows for a spatial prognosis of occurrence probabilities for Neandertal sites. External validation using a spatial artefact dataset for the German Middle Paleolithic shows generally good agreement.