The present study defines the organization of the mouse serum amyloid A (Saa) gene cluster on chromosome 7. A polymerase chain reaction (PCR)-based strategy was used successfully to generate a complete map of the mouse Saa genes, defining a linkage group of 3'-Saa2-5'/5'-Saa1-3'/5'-Saa4-3'/5'-Saa5-3'/5'-+ ++Saa3-3', with a maximum size of 45 kilobases (kb). This contrasts with the 150 kb human SAA gene cluster, which has been previously defined. The tight linkage of both mouse Saas and human SAAs is of potential functional significance, since the genes that encode the acute phase serum amyloid A proteins are known to exhibit co-ordinate transcriptional regulation. The present results thus suggest that selective pressure may exist which maintains the co-ordinately transcribed Saa genes in close physical proximity. This study, furthermore, demonstrates the utility of a novel PCR-based approach for fine mapping of tightly clustered linkage groups. The strategy used possesses a number of advantages over previously described techniques, such as long-range restriction mapping, since it facilitates the concurrent determination of not only precise relative map positions, but also the relative transcriptional orientations of assayed paired loci. Although presently limited in resolution to genes not more than 27 kb apart, future technical advances are likely to extend the applicability of this approach in mapping experiments to less tightly linked clusters of genes.