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This paper explores efficiency of primary and lower secondary schools in Italy from a productivity perspective, where inputs are variables directly related to the allocation of human and financial resources of schools and output variables measuring the level of educational achievements in mathematics and reading, from the INVALSI national assessment. The analysis is conducted on a statistical sample of more than a thousand primary and lower secondary schools using non-parametric techniques of data envelopment analysis (DEA). Given the multiple outputs and multiple inputs and the lack of a specific assumption on the form of the function relating outputs to inputs, DEA is better suited for estimation of the relative efficiency of schools than its parametric counterparts. Bias-corrected efficiency scores obtained with bootstrap procedures show how, despite an overall high average level of efficiency, there are relevant differences between schools. Empirical results confirm, in general, the influence of the local context on school efficiency and the beneficial effect of factors like the share of tenured teachers and, in some specifications, of investment expenditure. However an unexpected negative impact comes from specific organization features: comprehensive schools including both primary and lower secondary education seem to be less efficient than schools that specialize in one or the other segment. This result deserves some attention, especially in the view of a recent decree law (n. 98/2011) which provides for the fusion of all primary and lower secondary schools into comprehensive schools. However, comprehensive schools turn out to be characterized by a greater dispersion of service delivery points (sometimes even located in different municipalities). This requires major coordination efforts and does not necessarily translate in a lower rate of personnel per student compared to the specialized schools, nor in much better results.