Candida albicans infection is a significant cause of morbidity and mortality in immunocompromised patients. In vivo and in vitro models have been developed to study both the fungal and the mammalian immune responses. Phagocytic cells (i.e., macrophages) play a key role in innate immunity against C. albicans by capturing, killing and processing the pathogen for presentation to T cells. The use of microarray technology to study global fungal transcriptional changes after interaction with different host cells has revealed how C. albicans adapts to its environment. Proteomic tools complement molecular approaches and computational methods enable the formulation of relevant biological hypotheses. Therefore, the combination of genomics, proteomics and bioinformatics tools (i.e., network analyses) is a powerful strategy to better understand the biological situation of the fungus inside macrophages; part of the fungal population is killed while a significantly high percentage survives.