In this article, I explore some of the epistemological, technical, and ethical challenges in doing research on instructed second language (L2) learning in Canadian school settings. I examine these challenges from the viewpoint of classroom research that has been influenced by cognitive-interactionist theories of learning. This includes my own classroom research program and similar programs developed by other Canadian researchers across a variety of school-based L2 curricula. I examine epistemological challenges in terms of the ecological validity of doing research in classrooms versus laboratories and the value of sequencing descriptive phases prior to experimental components of a research cycle. I also discuss the extent to which different research contexts and goals can influence epistemological choice. In addition, I consider technical challenges in relation to doing research in intact classrooms and to the conditions necessary for the development of sustained research programs in schools. Lastly, I address ethical challenges: the relevance of research for pedagogical practice and suggestions about how to support researchers and teachers in making these links more meaningful.