1) A Mexican family with familial hypercholesterolemia (FH) linked to chromosome 1p32 was found to also have elevated HDL-C (high-density lipoprotein cholesterol) linked to chromosome 6p, which protected against atherosclerosis despite FH. 2) The FH trait mapped to chromosome 1p32, a region previously linked to FH, while the elevated HDL-C trait mapped to chromosome 6p, a region not previously linked to FH. 3) This family provides evidence that a locus on chromosome 6p confers an anti-atherogenic effect exceeding its effect on cholesterol levels, and may protect against risk factors beyond FH like hypertension and smoking.