We have previously shown that the nuclear-encoded gene’s expression of mitochondrial β-subunit of the F1-ATPase complex in rat liver is regulated at the translational level (Luis, A.M., Izquierdo, J.M., Ostronoff, L.K., Santaren, J., Salinas, M., and Cuezva, J.M. (1993) J. Biol. Chem. 268, 1868-1875). In this paper we report that the different steady-state levels of ATP synthase β subunit mRNA detected in rat tissues are not paralleled by a proportional content of immunodetectable β-F1-ATPase protein. The results suggest that tissue-specific transcriptional and post-transcriptional mechanisms contribute to differential mitochondrial biogenesis in mammalian cells. On the other hand, steady-state mRNA levels of the mitochondrial encoded ATP synthase subunits (ATP 6 + 8) indicate that nuclear and mitochondrial-encoded transcripts for this complex are in close relation, that is, the expression of both nuclear and mitochondrial genes is coordinated in all tissues examined. © 1993 Academic Press, Inc.