We examine the two-loop QCD corrections to the neutral Higgs masses in the MSSM by performing the full diagrammatic computation of the top/stop contributions in a mixed OS/DRbar scheme. We include novel results for the corresponding O(alpha alpha_s) corrections. The explicit shifts of the Higgs self-energies with respect to their effective potential counterparts are given in terms of a set of master integrals. The master integrals which are not yet known in analytic form are evaluated numerically with the fast computer code TSIL. All our results are expressed in terms of low energy physical parameters and can be readily included in the existing packages for phenomenological studies.