Research into the major fungal pathogen, Candida albicans has firmly entered the post-genomics era. The current challenge is to apply these technologies to the analysis of C. albicans infections. Initial studies, which focused on the expression of specific virulence genes, have supported the view that secreted hydrolases and adhesins are expressed in a niche-specific fashion during infection. However, genome-wide expression profiling has revealed that most infection-related changes in C. albicans gene expression reflect environmental adaptation. Initial contacts with the host and disease progression are clearly associated with metabolic and stress adaptation. These studies, together with analyses of C. albicans mutants, indicate that physiological fitness plays a central role in the pathogenicity of this fungus, alongside virulence factors.