New radiometric and magnetostratigraphic data from Quillagua and Calama basins (Atacama desert) indicate that the stratigraphic record over the last 10 Ma includes two hiatuses, lasting approximately 2 and 4 million years respectively. These sedimentary gaps are thought to represent prolonged periods of hyperaridity in the region, with absence of sediment production and accumulation in the central depressions. Their remarkable synchrony with Antarctic and Patagonian glacial stages, Humboldt cold current enhancement and cold upwelling waters lead us to suggest long-term climate forcing. Higher frequency climate (orbital precession and eccentricity) forcing is thought to control the sequential arrangement of the lacustrine units deposited at times of lower aridity. Hyperaridity trends appear to be modulated by the activity of the South American Summer Monsoon, which drives precipitation along the high altitude areas to the east of Atacama. This precipitation increase combined with the eastward enlargement of the regional drainage during the late Pleistocene enabled water transfer from these high altitude areas to the low lying closed Quillagua basin and resulted in the deposition of the last widespread saline lacustrine deposits in this depression, before its drainage was open to the Pacific Ocean.