Photorhabdus luminescens is an insect pathogen associated with specific soil nematodes. The bacterium has a complex life cycle with a symbiotic stage in which bacteria colonize the intestinal tract of the nematodes, and a pathogenic stage against susceptible larval-stage insect. Symbiosis-"deficient" phenotypic variants (known as secondary forms) arise during prolonged incubation. Correspondence analysis of the in silico proteome translated from the genome sequence of strain TT01 identified two major biases in the amino acid composition of the proteins. We analyzed the proteome, separating three classes of extracts: cellular, extracellular, and membrane-associated proteins, resolved by 2-DE. Approximately 450 spots matching the translation products of 231 different coding DNA sequences were identified by PMF. A comparative analysis was performed to characterize the protein content of both variants. Differences were evident during stationary growth phase. Very few proteins were found in variant II supernatants, and numerous proteins were lacking in the membrane-associated fraction. Proteins up-regulated by the phenotypic variation phenomenon were involved in oxidative stress, energy metabolism, and translation. The transport and binding of iron, sugars and amino acids were also affected and molecular chaperones were strongly down-regulated. A potential role for H-NS in phenotypic variation control is discussed.