Rhizobium etli undergoes a transition from an aerobic to a fermentative metabolism during successive subcultures in minimal medium. This metabolic transition does not occur in cells subcultured in rich medium, or in minimal medium containing either biotin or thiamine. In this report, we characterize the aerobic and fermentative metabolism of R. etli using proteome analysis. According to their synthesis patterns in response to aerobic (rich medium, minimal medium with biotin or minimal medium with thiamine) or fermentative (minimal medium without supplements) growth conditions, proteins were assigned to five different classes: (i) proteins produced only in aerobic conditions (e.g., catalase-peroxidase KatG and the E2 component of pyruvate dehydrogenase); (ii) protein produced under both conditions but strongly induced in aerobic metabolism (e.g., malate dehydrogenase and the succinyl-CoA synthetase beta subunit); (iii) proteins that were induced equally under all conditions tested (e.g., AniA, DnaK, and GroEL); (iv) proteins downregulated during aerobic metabolism, and (v) proteins specific to only one of the conditions analyzed. Northern blotting studies of katG expression confirmed the proteome data for this protein. The negative regulation of carbon metabolism proteins observed in fermentative metabolism is consistent with the drastic physiological changes which occur during this process.