Previous studies have shown that distal mouse chromosome 1 contains the apolipoprotein AII (apoAII) gene, encoding the second most abundant apolipoprotein in high density lipoproteins (HDLs), as well as a gene termed Ath-1 that controls aortic fatty streak development and HDL cholesterol levels in response to a high-fat, high-cholesterol diet. We report genetic studies confirming that the genes are distinct. Using molecular markers for mouse chromosome 1, we have further mapped the two genes, and our results indicate that they are separated by a minimum of 2 cM. We also report evidence that in mice on a low-fat chow diet, the apoAII gene locus influences HDL cholesterol levels. Thus, statistical analysis of two sets of recombinant inbred strains revealed concordant segregation patterns of HDL cholesterol levels and the apoAII gene locus. The effect of apoAII expression on HDL cholesterol levels was further tested by using a congenic strain that exhibits increased apoAII synthesis in comparison to the background strain. The results support the concept that increased synthesis of apoAII results in increased HDL cholesterol levels. Unexpectedly, increased expression of apoAII appeared to promote rather than retard aortic fatty streak development.