Because proteins are key effectors of plant responses to environmental cues including recognition, signalling, transport and defence reactions, main interest has been paid to characterize those involved in the establishment and functioning of arbuscular mycorrhizal (AM) symbiosis. In our group, the setting up of high throughput proteomic techniques on the model species, Medicago truncatula, is providing step-by-step a large-scale analysis of AM symbiosis-related proteins. Depending on the symbiotic stage targeted and on the abundance of mycorrhizal material, different proteomic strategies that can be combined with other large-scale approaches (transcriptomic and metabolomic) will be presented. Modification of the M. truncatula root proteome during the early stage of AM symbiosis has been investigated by comparing the protein patterns obtained from non-inoculated roots and roots synchronized for appressorium formation in wild-type (J5), penetration-defective (TRV25, dmi3) and autoregulation-defective (TR122, sunn) genotypes. In mature mycorrhiza, sub-cellular proteomic approaches have been developed in M. truncatula to target symbiosis-related membrane proteins eligible as involved in nutrient transport and signalling between symbionts upon arbuscule formation. In addition, with the aim of determining overlaps in response to the two most commonly employed AM fungal isolates we recently launched a high throughput comparative proteomic analysis. The future release of the genome sequencing programs launched for M. truncatula and Glomus intraradices is likely to provide additional knowledge about AM symbiosis-related proteins.