Hormone-sensitive lipase (HSL) catalyzes the intracellular hydrolysis of triacylglycerols and cholesteryl esters, and it is involved in regulating body fat, steroidogenesis, and insulin secretion. Thus, genetic variability at the HSL locus (LIPE) may play a significant role on lipid metabolism and the risk of obesity and type 2 diabetes. Therefore, we have examined two LIPE single nucleotide polymorphism (SNP) [14672C>G in the promoter region and 17948C>T (rs1206034) on intron 2] in relation to plasma lipids, anthropometrical and glucose-related phenotypes in a population of mostly overweight and obese men (373) and women (361). In women, the 17948T allele was associated with decreased total cholesterol (TC, p = 0.001), LDL-cholesterol (LDLc, p < 0.001) and apoE concentrations (p = 0.041). Conversely, female carriers of the LIPE 14672G allele had significantly higher TC (p = 0.047), LDLc (p = 0.041), and apoE (p = 0.041) levels. Although we did not find significant associations in men, we observed that male carriers of the LIPE 14672G who did not drink alcohol showed higher glucose levels than non-carriers (p = 0.008), whereas there were no allele-related differences among drinkers (p = 0.019 for the interaction). These SNPs were not significantly associated with anthropometrical variables. In summary, variation at this locus showed gender-specific associations with lipids and glucose measures, and the latter was influenced by alcohol drinking.