The sequencing of the Candida albicans genome and recent refinements in protein resolution and identification techniques have greatly enhanced the application of proteomics for the study of this fungal pathogen. Proteome analysis includes the separation and isolation of proteins by two-dimensional polyacrylamide gel electrophoresis and subsequent protein identification by peptide mass fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. This technique has been used for the study of the proteomes of Candida species in the context of virulence, drug response, and resistance. We describe here the application of this approach to the study of azole antifungal resistance in C. albicans .