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Paleoclimate records from the Atacama Desert are rare and mostly discontinuous, mainly recording runoff from the Precordillera to the east, rather than local precipitation. Until now, paleoclimate records have not been reported from the hyperarid core of the Atacama Desert (<2 mm/yr). Here we report the results from multi-disciplinary investigation of a 6.2 m drill core retrieved from an endorheic basin within the Coastal Cordillera. The record spans the last 215 ka and indicates that the long-term hyperarid climate in the Central Atacama witnessed small but significant changes in precipitation since the penultimate interglacial. Somewhat 'wetter' climate with enhanced erosion and transport of material into the investigated basin, commenced during interglacial times (MIS 7, MIS 5), whereas during glacial times (MIS 6, MIS 4-1) sediment transport into the catchment was reduced or even absent. Pelagic diatom assemblages even suggest the existence of ephemeral lakes in the basin. The reconstructed wetter phases are asynchronous with wet phases in the Altiplano but synchronous with increased sea-surface temperatures off the coasts of Chile and Peru, i.e. resembling modern El Nino-like conditions.