The low-density lipoprotein receptor (LDLR) plays a pivotal role in cholesterol homeostasis. However, the role of genetic variations in the 3' UTR of the LDLR in relation to plasma cholesterol has been largely understudied. Six SNPs, G44243A, G44332A, C44506G, G44695A, C44857T and A44964G, within the 5' region of the 3'UTR fall into three common haplotypes, GGCGCA, AGCACG, and GGCGTA, occurring at frequencies of 0.45, 0.31 and 0.17 respectively in Caucasians (n=29) and 0.13, 0.13 and 0.38 respectively in African Americans (n=32), with three other haplotypes occurring at lesser frequencies. Genotyping of two "haplotype tagging" SNPs, C44857T and A44964G, in the Atherosclerosis Risk in Community (ARIC) study population showed that in Caucasians, but not in African Americans, the inferred TA haplotype had a significant LDL-cholesterol lowering effect. The adjusted LDL-cholesterol levels in the TA/TA diplotypes were lower by 6.10 mg/dl in men (P<0.001) and by 4.63 mg/dl in women (P<0.01) than in individuals with other diplotypes. Caucasian men homozygous for CA, in contrast, showed significantly higher LDL-cholesterol (P<0.04), lower HDL-cholesterol (P<0.02) and higher LDL/HDL ratios (P<0.001). To identify if these haplotypes are causative, we studied the expression of a reporter gene in a tissue culture based system carrying a 3'UTR that includes the 1kb nucleotide sequences corresponding to the AGCACG, GGCGTA and GGCGCA haplotypes. The three haplotypes of the 3'UTR sequences had no difference in their effect on the expression. Therefore, the association in Caucasians with plasma lipid profiles indicative of higher cardiovascular risk is not caused by polymorphisms in the 3'UTR of the LDLR gene, but with other polymorphisms that are in linkage disequilibrium with them.