After the genomic sequence of Saccharomyces cerevisiae was published in 1996, various fungi were investigated from the viewpoint of the genomic analysis. In the following five years, the progress of genomic research was particularly evident in the field of pathogenic fungi. With the help of the proteomic and the transcriptomic analyses researchers nowadays can use the new genome information as a powerful tool for the search of fungal virulence factors and new targets of the anti-fungal agents. In this review, we outlined the recent progress in genomic analysis of fungi and the proteomic and transcriptomic analyses in the field of medical mycology.