Candida albicans is an opportunistic fungus which causes both superficial infections and life-threatening systemic candidiasis in immunocompromised hosts such as AIDS patients, people with cancer, or other immunosuppressed individuals. Virulence factors for this fungus include the ability to adhere to host tissues, production of tissue damaging secreted enzymes, and changes in morphological form that may enhance tissue penetration and avoidance of immune surveillance. Treatment of candidiasis patients is hampered by a limited choice of antifungal agents and the appearance of clinical isolates resistant to azole drugs. Proteome analysis involves the separation and isolation of proteins by two-dimensional gel electrophoresis and their identification and characterization by mass spectrometry. The systematic application of this methodology to C. albicans is in its infancy, but is progressing rapidly. Comparing protein profiles between avirulent and virulent C. albicans strains, between drug-sensitive and -resistant strains, or between different morphological forms, could identify key control and effector proteins. There are difficulties, however, associated with the display of low abundance and cell envelope-associated proteins and the choice of conditions for obtaining suitable C. albicans cells. This article describes the potential of applying proteome analysis to C. albicans in order to better understand pathogenicity and identify new antifungal targets.