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We investigated top and bottom exchange biased perpendicularly magnetized magnetic tunnel junctions (pMTJs) with IrMn and the effects of the multilayer structure on the magnetoresistance and perpendicular exchange bias. The TMR ratio of the top exchange biased (TEB)-pMTJ was significantly deteriorated compared with that of the pseudo-pMTJ, due to the high junction resistance and the in-plane anisotropy induced in the Co/IrMn interface. The TMR ratio and perpendicular exchange bias were improved in the bottom exchange biased (BEB)-pMTJ as compared with those of the TEB-pMTJ. Perpendicularly magnetized buffer layers, such as (Pd/Co)n, should be used to induce perpendicular exchange coupling with antiferromagnets such as IrMn in BEB-pMTJs.