The use of fixed (FE) and random effects (RE) in two-level hierarchical linear regression is discussed in the context of education research. We compare the robustness of FE models with the modelling flexibility and potential efficiency of those from RE models. We argue that the two should be seen as complementary approaches. We then compare both modelling approaches in our empirical examples. Results suggest a negative effect of special educational needs (SEN) status on educational attainment, with selection into SEN status largely driven by pupil level rather than school-level factors.