The Atacama Desert is one of the driest deserts on Earth with a predominantly hyperarid climate at least since the Miocene. Geological evidence, however, indicates that this overall hyperaridity was repeatedly interrupted by wetter periods. Deep-time precipitation reconstructions of the Atacama Desert are limited by scarce and discontinuous sediment sequences, most of which received moisture from wetter regions outside the Atacama Desert. Longer archives of the precipitation history in the desert interior during the Neogene are unfortunately extremely rare. The sediment records of two tectonically blocked endorheic basins (a.k.a clay pans) in the Coastal Cordillera of northern Chile may fill the gaps in the paleo-precipitation record of the Atacama Desert. Comprehensive investigations of both clay pans applied intensive geological and geophysical site surveys and deep drilling operations with subsequent downhole logging. Short pilot cores of up to 6.2 m in length already showed highly variable sediment successions reflecting strong hydroclimatic fluctuations on glacial/interglacial timescales. Electromagnetic and seismic surveys yielded a three-layer structure in both basins consisting of the resistive basement overlain by a low-resistivity basal and a highly resistive upper sediment unit with total sediment thicknesses of more than ∼100 and ∼160 m in the Playa Adamito Grande (PAG) and Paranal clay pans, respectively. Assuming similar sedimentation rates as the pilot cores, this would imply that the sediment records of both clay pans span several million years. Lithological data and downhole-logging results of the deep-drilling operations reveal strong heterogeneities in the sediment composition that presumably can be traced back to major climatic and/or tectonic shifts in the catchments of the clay pans. Whereas the fine-grained sediments at the base of the PAG sequence suggest longer-lasting lacustrine sedimentation with enhanced evaporative episodes, the lower sediment package in the core from the Paranal clay pan consists of fluvial conglomerates and sandstones. Both lacustrine and fluvial sediments indicate less arid conditions in the central Atacama Desert than today. Separated by distinct lithological boundaries, the upper sediments in both clay pans show several similar sediment facies typical for alluvial-fan deposition, e.g., proximal mud and debris flows, sheetfloods, and distal alluvial sediment flows, but also pedogenic calcium sulfates. The shift to a predominant alluvial-fan deposition, which is common after torrential rainfall in the Atacama Desert today, implies a general modification in the environmental conditions of the study areas. These initial results already highlight the potential of the sediment records from the PAG and Paranal clay pans to provide unprecedented information on the Neogene precipitation history in the hyperarid core of the Atacama Desert.