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First-principles density-functional calculations of the atomic and electronic structure of Co/SrTiO3 /Co (001) magnetic tunnel junctions (MTJ’s) are performed. Different interface terminations are considered and the most stable structure with the TiO2 termination is identified based on energetics of adhesion. The calculated electronic structure of the TiO2-terminated MTJ shows an exchange coupling between the interface Co and Ti atoms mediated by oxygen. This coupling induces a magnetic moment of 0.25 µB on the interface Ti atom, which is aligned antiparallel to the magnetic moment of the Co layer. We argue that this might cause an inversion of the spin polarization of tunneling across the SrTiO3 barrier which was found in recent experiments.