Infectious diseases represent a major health problem worldwide, both in terms of morbidity and mortality. A complex combination of environmental, pathogen and host genetic factors plays a role in determining both susceptibility to particular microbes and the course of infection. Numerous studies have now mapped and identified relevant genes using a variety of both family-based and population-based approaches. Much interest has been focused on susceptibility to malaria, HIV/AIDS and mycobacterial infection, but other bacterial, viral and parasitic diseases are receiving increasing attention. Some major genes have been identified by genome scans of multi-case families, and mouse genetics has contributed to mapping and identification of a few genes. However, the great majority of known susceptibility loci emerged from screening of likely candidate genes. The emerging picture is of highly polygenic diseases, with occasional major genes, along with significant inter-population heterogeneity. This genetic architecture likely reflects the role that evolutionary selection has played in generating and maintaining a diverse repertoire of susceptibility/resistance loci, most with individually small effects. Genome-wide association studies with large sample sizes will be required to define the majority of the relevant polygenes.