Systematic mutagenesis of large viral genomes such as those of the cytomegaloviruses requires strategies for identifying relevant functions as well as for detailed analysis of particular genes. A number of genetic markers that have been developed in other biological systems have been useful for insertion mutagenesis in these viruses. Thus far, 57 of the over 227 genes carried by wild-type human cytomegalovirus have been found to be dispensable for growth in cultured cells. Because of the limitations on studying human cytomegalovirus in an animal host, the closely related murine cytomegalovirus has been used as a surrogate for pathogenesis, tissue tropism and latency studies in the laboratory mouse. Genetic analysis of this virus has paralleled work on human cytomegalovirus, and an understanding of genes that specifically impact viral growth in particular organs has emerged from these studies. Strategies for generation of permissive cell lines able to complement essential human cytomegalovirus replication functions have been described, and sets of cosmid clones have been used to generate recombinant viruses. These methods will enable a systematic functional analysis of the genomes of human and animal cytomegaloviruses.