Penicillium marneffei is a dimorphic fungus endemic in southeast Asia. The incidence of P. marneffei infection has increased greatly in this region with the spread of human immunodeficiency virus, but the infection routes and pathogenic mechanisms of P. marneffei remain poorly understood. P. marneffei is an opportunistic human pathogen exhibiting a temperature-dependent dimorphic switch. At 25 degrees C it grows as filamentous hyphae, whilst at 37 degrees C it forms uninucleate yeast cells and divides by fission. Dimorphic fungal pathogenicity is frequently associated with the dimorphic switch, but the mechanism that regulates the switch has remained obscure. In this report, two-dimensional difference gel electrophoresis was used to investigate the proteins expressed differentially in the yeast and mycelial phases of a wild-type isolate of P. marneffei. Among thousands of protein molecules displayed, more than 500 showed differential expression between the two phases. In particular, 26 proteins were identified using matrix-assisted laser desorption/ionization time-of-flight MS. Expression of catalase-peroxidase, isocitrate lyase, Hsp90, binding protein and cytochrome P-450 increased significantly in the yeast phase, whereas levels of poly(A) polymerase and SNF22 were reduced.