In this paper, we have outlined some of the methodological dilemmas we have encountered in conducting a qualitative, longitudinal study of secondary students. These dilemmas have ethical, epistemological and pragmatic implications, and they were discussed in terms of both macro or foundational methodological issues, as well as questions and problems specific to our project. We argued, however, that being sensitive to these various dilemmas, acknowledging their validity and cautions, and integrating them within the design, carrying out and interpretation of the research does not preclude the possibility of conducting empirical research that builds new knowledge and understandings, about, in this instance, young girls and boys and schooling today. The second half of the paper elaborated some of our concerns about the strategies for investigating processes of gender construction, and provided some examples of how we have begun to read our findings about the way in which girls and boys are working out and enacting the construction of gender.