Differentiated instruction is a teaching philosophy and practice that deals with responding appropriately to student heterogeneity. In order to gain deep understanding of this complex concept, research methodology is challenged to use appropriate data collection and data analysis. The aim of this paper is to reflect on how system theory may be used as ontological and epistemic grounding for research on differentiated instruction. Three challenges for this research are presented: to focus on the interplay between the individual and complex collective behaviour; to acknowledge the external influences in research design; and to describe patterns of non-linear causality and emergence. Three design principles for research on differentiated instruction are presented to address these challenges: organic design, interaction and reflectivity. By using these principles, we believe research on differentiated instruction would be aligned with the theoretical foundations of the concept.