We have explored the correlation between the Seebeck coefficient and the electronic structure of nanostructured rutile MnO2 using density functional theory to critically appraise the three orders of magnitude scatter in literature data. Our hypothesis is that the microstructure and morphology on the nanoscale is causing this behaviour, which we have tested by comparing the Seebeck coefficient of bulk MnO2 with two low-energy surfaces: MnO2(1 1 0) and MnO2(0 0 1). From these data, it is evident that variations over two orders of magnitude in the Seebeck coefficient can be attained by affecting domain size and texture on the nanoscale. This may be understood by analysing the electronic structure. Surface hybridized Mn d-O p states fill the band gap of MnO2 and thus substantially alter the transport properties.