Prior genetic and physical mapping has shown that theNaipgene cluster on mouse chromosome 13D1-D3 contains a gene,Lgn1, that is responsible for determining the permissivity of ex vivo macrophages toLegionella pneumophilareplication. We have identified differences in the structure of theNaiparray among commonly used inbred mouse strains, although these gross structural differences do not correlate with differences inL. pneumophilapermissiveness. A physical map of the region employing clones of the C57BL/6J haplotype confirms that there are fewer copies ofNaipin this strain than are in the physical map of the 129 haplotype. We have also refined the genetic location ofLgn1, leaving onlyNaip2andNaip5as candidates forLgn1. Our genetic map suggests the presence of two hotspots of recombination within theNaiparray, indicating that the 3′ portion ofNaipmay be involved in the genomic instability at this locus.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.AF240489–AF240530.]