Quantitative secondary analysis of large-scale data can be combined with in-depth qualitative methods. In this paper, we discuss the role of this combined methods approach in examining the uptake of physics and chemistry in post compulsory schooling for students in England. The secondary data analysis of the National Pupil Database (NPD) served three distinct purposes in the design of this study. These included (1) determining the number of students in England who went on to take physics and chemistry post 16, (2) examining associations between school-level factors and physics and chemistry uptake, and (3) using the secondary data analysis to construct a sampling frame for the selection of the case study schools. Findings from the analysis of the NPD are presented along with a discussion of the limitations and advantages of using large-scale secondary data analysis in a combined methods study. (Contains 13 notes, 2 figures, and 3 tables.)