Combined strontium and neodymium isotope data on the Miocene-Pliocene Cordillera Blanca batholith (9–11 °S) are compared with acid plutonic and volcanic rocks of similar age and composition from the central Andes (ca. 16–23 °S). Although intruded through 50–60 km of continental crust the batholith rocks, which range in composition from quartz diorite to high silica leucogranodiorite, show little sign of contamination by mature continental basement. Initial 87Sr 86Sr ratios define a range of 0.7041 to 0.7057, with average ϵ Nd values close to bulk earth (−0.5), over a relatively large range in SiO 2. It is difficult to reconcile the isotopic composition of the batholith rocks with simple AFC models involving fractionation of either clinopyroxene (deep-level) or plagioclase (high-level) dominated assemblages, and the isotopic variation in these rocks is instead considered to be inherited from a primary subcontinental lithosphere source through a two-stage process of crustal underplating and subsequent partial melting. Estimated (mantle) magma production rates during underplating are 0.1–0.3 km 3 yr −1. Comparisons with Miocene plutonic rocks from the western and eastern Cordillera at ~ 11 °S show no clear trends in isotopic compositions in time or space. Furthermore, the isotopic compositions of Nd and Sr in the batholith rocks contrast strongly with basaltic to high silica volcanic and plutonic rocks of similar age exposed in the central Andes, where 143Nd 144Nd and 87Sr 86Sr are thought to reflect contamination of mantle-derived magmas and/or tectonic reworking of old basement material during crustal thickening. The lack of significant involvement of basement material in the petrogenesis of the batholith magmas may be due to differences in the mechanism of crustal thickening along the Andean chain during the Late Miocene, with thickening in the central Andes being caused predominantly by tectonic shortening, while in northern-central Peru thickening occurred mostly through crustal underplating of mantle-derived basalt. These two regions thus represent first-order crustal domains in the central Andean Cordilleras. The boundary between them is marked by the Abancay Deflection.