There is much research on the role of theory in mathematics education research, at least from more overarching or theoretical perspectives. Micro analyses of the role of theory in particular research studies are rarer. We contribute by analysing one empirical study to allow for in-depth analyses and discussions around the role of theory in a specific case, concerning relationships between mathematics and reading. Our results show that studies that do not use an explicit theoretical model can still be strongly influenced by implicit theoretical assumptions. We conclude that it is important to identify existing theoretical assumptions in an empirical research study and try to convey them as clearly as possible, and we discuss specific issues concerning research on relationships between mathematics and reading.