The purpose of this paper is to compare the efficiency of the Spanish public and publicly-subsidised private high schools using Data Envelopment Analysis (DEA) fed by the results provided by a hierarchical linear model (HLM) applied to PISA-2006 (Programme for International Students Assessment) microdata. This study places special emphasis on the estimation of the determinants of school outcomes, the educational production function being estimated through an HLM that takes into account the nested nature of PISA data. Inefficiencies are then measured through the DEA and decomposed into managerial (related to individual performance) and programme (related to structural differences between management models), following Silva Portela and Thanassoulis (2001) approach. Once differences in pupils’ background and individual management inefficiencies have been eliminated, results reveal that Spanish public high schools are more efficient than publicly-subsidised private ones