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First-principles calculations based on density functional theory are used to elucidate the effect of O vacancies, forming F centers, on spin-dependent tunneling in Fe/MgO/Fe(001) magnetic tunnel junctions. O vacancies produce occupied localized s states and unoccupied resonant p states, which is consistent with available experimental data. The authors find that O vacancies affect the conductance by nonresonant scattering of tunneling electrons causing a substantial reduction of tunneling magnetoresistance (TMR). Improving the quality of the MgO barrier to reduce O vacancy concentration would improve TMR in these and similar junctions.