© Copyright 2015, Mary Ann Liebert, Inc. 2015. HIV-infected patients treated with highly active antiretroviral therapy (HAART) may be predisposed to a lipid profile, associated with increased cardiovascular risk, derived from having high triglycerides (TG) and low high-density lipoprotein cholesterol (HDLc) levels. We propose that genetic variability leaves some HIV-infected patients more predisposed to this lipid profile than others. We performed a cross-sectional, observational study including 321 antiretroviral-treated HIV-infected patients classified as normolipidemic (n=173) or presenting with high TG (≥1.7mmol/liter) and low HDLc [<1.02 (men) or 1.28mmol/liter (women)] (n=148) to investigate the impact of 13 polymorphisms of 9 genes affecting lipid metabolism (APOA5, APOC3, LPL, CETP, HL, MTP, APOE, LRP5, and VLDLR genes). The polymorphism rs328 in LPL was 40% significantly more frequent in normolipidemics (p=0.018), and in the same group, polymorphisms rs708272 in CETP and rs1800588 in HL were 10% significantly more frequent (p=0.037 for both polymorphisms). Patients who presented a combination of one to six alleles from these polymorphisms had 10% increased HDLc levels [1.13 (0.40) vs. 1.24 (0.23) mmol/liter, p=0.002] and a trend toward lower triglycerides [2.23 (2.34) vs. 1.89 (1.24) mmol/liter] and lower remnant-like particle cholesterol (RLPc) [16.41 (11.42) vs. 12.99 (11.69) mmol/liter]. This effect was dependent on the number of protective alleles and independent of the regimen administered. Polymorphisms in LPL, CETP, and HL protect HIV-infected patients from developing the dyslipidemia derived from high TG and low HDLc levels in a dose-dependent manner.