This article reflects on the place of RE in a pillarised education context, taking into account the fact of religious diversity and pluralisation among the school population on the one hand, and the freedom of religion and education of faith-based schools on the other. Particular attention will be given to Belgium and the Netherlands, which do not only have a comparable pillarised education model, but also have a quite similar religious landscape. After a brief historical sketch of the educational systems in both nations, attention will be given to the present situation and to the challenges of religious diversity and secularism in faith-based schools. In order to meet these challenges, recent developments concerning RE in Belgium and the Netherlands are discussed. In conclusion, we will outline some suggestions for the future of RE in faith-based schools in a pillarised education context.