Research on special needs education is often very complex and puts specific demands on the methodology used. Data-triangulation, at the very least, is required. In most of our recent research projects on the development of special needs education in Flanders (the Dutch speaking part of Belgium), we have made use of qualitative case studies to describe and understand the complex reality of the innovations taking place in our schools. In this article we discuss some methodological aspects of qualitative case study designs, illustrated with a study on the implementation of inclusive education in Flemish primary schools.