This article describes how Critical Communicative Methodology (CCM) has been used successfully to analyse educational inequalities in ways that generate real transformation towards social justice. We begin by arguing that educational research today should employ new methodological approaches that can ensure the inclusion of different voices in social science research and the production of knowledge that transforms social exclusion. We then analyse the main epistemological positions of CCM, based on Habermas' communicative action theory, and explain how it was implemented in the European Union-funded INCLUD-ED project. Finally, we illustrate how INCLUD-ED has had a social and political impact and we argue that research "with" vulnerable groups, based on the principles of CCM, can generate social and educational transformation.