Recent advances in next generation sequencing techniques have dramatically increased the availability of genomic data. Due to their relatively small genome size and importance as human and crop pathogens, over one hundred fungal genomes have been completely sequenced and published to date. This number is expected to increase dramatically over the coming years with individual institutions sequencing their own fungi of interest and the initiation of an ambitious project to sequence 1000 neglected fungal genomes (http://1000.fungalgenomes.org/). Currently a significant proportion of the available genomes are human pathogens as well as closely related non-pathogenic species. This type of data allows us to perform comparative genomic analyses between pathogenic and non-pathogenic species in an effort to uncover molecular mechanisms related to disease. The availability of full genome sequences also allows us to investigate many evolutionary processes in fungi such as horizontal gene transfer, gene fusions/fissions and intron gains and losses. The following chapter will discuss a selection of key comparative genomic analyses that have been performed on a number of the most common human pathogens and also illustrate how complete fungal genomes have helped us understand some of the mechanisms that have shaped fungal evolution.