Genomic methods have had a major impact in clinical microbiology in the last decades. Microbial genomes are relatively small and therefore easier to characterise than human genomes. In both bacteriology and in virology, genomic methods have largely been used for molecular epidemiology, but also for molecular resistance testing of microorganisms. Targeted sequencing of predefined or isolated microorganisms was initially a dominant method but has gradually been supplemented with metagenomic diagnostics. Metagenomics aims at mapping all microorganisms - pathogenic as well as apathogenic - in a sample without determining in advance which agent(s) the analysis is targeting. Finally, there is also an increasing interest in mapping the significance of the microbiome, i.e. normal flora, both in health and disease.