The systematic application of next-generation DNA sequencing technologies has provided detailed insights into the genomics of corynebacteria. The genomes of 13 Corynebacterium diphtheriae strains isolated from cases of classical diphtheria, endocarditis and pneumonia were completely sequenced and annotated, providing first insights into the pan-genome of this species. Comparative gene content analyses revealed an enormous collection of variable pilus gene clusters relevant for adhesion properties of C. diphtheriae. Variation in the distributed genome is apparently a common strategy of C. diphtheriae to establish differences in host-pathogen interactions. Molecular data deduced from the complete genome sequences of two Corynebacterium ulcerans strains provided considerable knowledge of candidate virulence factors, including a novel type of ribosome-binding protein with striking structural similarity to Shiga-like toxins. Likewise, functional data deduced from the complete genome sequences of six Corynebacterium pseudotuberculosis isolates from various sources greatly extended the knowledge of virulence factors and indicated that this species is equipped with a distinct gene set promoting its survival under unfavorable environmental conditions encountered in the mammalian host.