The proteome of the model symbiotic bacterium, Sinorhizobium meliloti was examined to determine the enzymatic reactions and cell processes that occur when S. meliloti occupies the root nodules of Medicago truncatula and Melilotus alba. The proteomes of the nodule bacteria were compared to that of S. meliloti grown under laboratory cultured conditions as an additional control. All the detectable protein spots on the two-dimensional (2-D) gels between pH 4-7 were analyzed. In total, the identity of proteins in 1545 spots from 2-D gels was determined using peptide mass fingerprinting. There were clear differences in the proteome of nodule bacteria and cultured bacteria and putative nodule-specific and nodule suppressed proteins were identified. The data were analyzed using metabolic pathway prediction programs and used to review the biochemical and genetic studies that had been done previously on S. meliloti over several decades. There was a broad congruency between the proteomic and biochemical data when the overall pathways of central carbon and nitrogen metabolism were considered. A selective suite of ABC-type transporters was present in nodule bacteria that were biased towards the transport of amino acids and inorganic ions (P and Fe) suggesting that a highly specialized nutrient exchange was occurring between the nodule bacteria and the host. Proteins prominent in nodule bacteria were those involved in the pathways for vitamin synthesis and stress-related processes (chaperoning, heat shock, detoxification of reactive oxygen species, regulation of stress and osmo-regulation). Some of these proteins were found only in nodule bacteria. These results show the extent of the shift in metabolism that occurs when S. meliloti invades legume plants and establishes a nitrogen fixing symbiosis.