Background-Elevated high-density lipoprotein cholesterol (HDL-C) is associated with reduced risk of cardiovascular disease, and variation in HDL-C levels has been shown to be Ϸ50% heritable. Overexpression of endothelial lipase (EL), a member of the lipoprotein lipase gene family, markedly reduces HDL-C levels in mouse models. We hypothesized that genetic variation in EL might be associated with elevated HDL-C. Methods and Results-All exons and 1.2 kilobase of promoter of the EL gene were sequenced in 20 unrelated human subjects with high HDL-C levels. A total of 17 variants were identified. Six of these were potentially functional and were confirmed by restriction enzyme analysis. Four variants result in amino acid changes (Gly26Ser, Thr111Ile, Thr298Ser, and Asn396Ser,) and 2 variants were in the promoter (Ϫ303A/C and Ϫ410C/G). The genotype frequencies of each variant were determined in 176 black controls, 165 white controls, and 123 whites with high HDL-C. The Thr111Ile variant was the most common, with an allele frequency of 10.3% in blacks, 31.2% in white controls, and 32.6% in the high HDL-C group. The remaining variants all had allele frequencies Ͻ5.0% but differed in frequency among the 3 groups. Interestingly, Gly26Ser, Thr298Ser, and Ϫ303A/C were found in the black and high HDL-C white cohorts but were absent in the control white group. Conclusions-Six new potentially functional variants in EL were discovered through sequencing of the EL gene in subjects with high HDL-C levels. Differences in allele frequencies exist between blacks and whites and between control subjects and those with high HDL-C levels. 2 Endothelial lipase (EL) is the most recently discovered member of the LPL, or triglyceride (TG) lipase, gene family. Cloned independently by 2 groups using distinct methods, 3,4 the EL gene spans 10 exons and 9 introns and encodes a polypeptide of 500 amino acids. The EL cDNA is 45% homologous to LPL and 40% to HL. Many of the regulatory domains found in LPL and HL, such as the lipoprotein and heparin-binding domains, are highly conserved in EL. 5 Unlike LPL and HL, EL is synthesized by endothelial cells and primarily acts as a phospholipase. 6 Whereas LPL activity indirectly influences the metabolism of high-density lipoprotein cholesterol (HDL-C) levels, 7 HL directly modulates the metabolism of HDL in vivo by converting larger HDL to smaller HDL. 2 Because EL acts predominantly as a phospholipase and the phospholipid content of HDL is a major factor in determining apolipoprotein A-I (apoA-I) conformation 8 and HDL function, 9 -11 we hypothesized that HDL might be a major substrate for EL. We showed that HDL is an excellent and preferred substrate for EL ex vivo. 6 Furthermore, we demonstrated that HDL-C and apoA-I levels were markedly reduced in mice injected with an adenoviral vector encoding human EL. 3 These results suggested that EL may play a central role in HDL metabolism.At least 50% of the variation in HDL-C is genetically determined. 12,13 Genetic diversity at both the LPL and HL loci ha...