It has been recognized that there is a need to conduct School Effectiveness Research (SER) in different countries and contexts since it has been mostly conducted in the US, the UK, the Netherlands and Australia (Peng, Thomas, Yang, & Li, 2006). Even some reviews on SER such as those reported by Scheerens (2001, 2004); Yu, (2007) are based on studies that fail to satisfy SER methodological requirements (Goldstein, 1997; Saunders, 1999). Rarer are studies in Portuguese speaking countries. This paper aims to provide evidence on school effects in the Portuguese and Brazilian primary education and to compare results to those reported in other countries. Research aspects explored in both countries are the magnitude of school effect, its stability over time and consistency between different contents. The influence of pupil socioeconomic background and prior achievement on student's learning outcomes through schooling trajectory is compared.