The use of proteomic tools allows a global and dynamic view of proteins that are expressed by bacteria. As an increasing number of bacterial genomes is currently available for homology searches, it is now possible to use such techniques to screen proteins expressed by microorganisms used in various fermented foods. Proteomic tools are also useful to investigate protein heterogeneity in protein-rich foods. In this paper the use of proteomic tools for the characterisation of milk proteins and in the study of protein expression of lactic acid bacteria used for manufacture of dairy products is reviewed; particular attention is given applied to advances in proteomic techniques available. The particular case of proteomics applied to cheese as an example of a complex food matrix [a mixture of animal (milk) and microbial proteins] is discussed, focusing on a novel strategy that allows the study of the enzymatic machinery found in situ in cheese.