Neogene through Pleistocene lava flows of the Nevados de Payachata region (lat 18°S) on the Altiplano of northern Chile fall into two discrete chemical groups defined by age and incompatible element concentrations. The Neogene suite (10.5-6.6 Ma) has trace element concentrations comparable to arc magmas erupted on thin crust in central Chile. Pleistocene lava flows (0.29-0 Ma) are enriched in incompatible elements relative to Neogene samples but have similar Sr, Nd, and Pb isotopic ratios. Incompatible element enrichment in mafic rocks reflects deep-crustal or subcrustal processes. Neogene volcanism in northern Chile immediately followed a period of intense crustal thickening. Uplift rates accelerated at ∼15 Ma, indicating that the "thin-crust"-type Neogene magmas actually traversed a thickened crust. The isotopic and trace element relations are the result of contamination of mantle-derived basalts in an upwardly growing lower-crustal interaction zone, defined to be the part of the lower crust at or above its solidus. Because the lower crust reaches postorogenic thermal equilibrium slowly, the lower-crustal interaction zone during Neogene magmatism had essentially the same thickness as it did prior to deformation. Thermal relaxation of the lower crust after thickening produced an upwardly growing column of crust near its solidus. Only 15 m.y. after crustal thickening did ascending, mantle-derived mafic magmas encounter previously unmelted, fertile crust near its solidus in the upper fringes of the interaction zone. Here the magmas were contaminated with incompatible element-enriched crustal melts, forming the parental magmas for the Pleistocene suite.