HIV-associated lipodystrophy (HIVLD) is a metabolic condition with an irregularity in the production of lipoprotein particles, and its occurrence varies among HIV-infected patients.MTPandABCG2genes have a role in the transport of lipoproteins. The polymorphisms ofMTP-493G/T andABCG234G/A affect its expression and influence the secretion and transportation of lipoproteins. Hence, we investigated theMTP -493G/T andABCG234G/A polymorphisms in 187 HIV-infected patients (64 with HIVLD and 123 without HIVLD) along with 139 healthy controls using polymerase chain reaction (PCR)-restriction fragment length polymorphism and expression analysis using real-time PCR.ABCG234A allele showed an insignificantly reduced risk of LDHIV severity [P= 0.07, odds ratio (OR) = 0.55].MTP-493T allele exhibited a non-significantly reduced risk for the development of dyslipidemia (P= 0.08, OR = 0.71). In patients with HIVLD, the ABCG234GA genotype was linked with impaired low-density lipoprotein levels and showed a reduced risk for LDHIV severity (P= 0.04, OR = 0.17). In patients without HIVLD,the ABCG234GA genotype was associated with impaired triglyceride levels with marginal significance and showed an increased risk for the development of dyslipidemia (P= 0.07, OR = 2.76). The expression level ofMTPgene was 1.22-fold decreased in patients without HIVLD compared with that in patients with HIVLD.ABCG2gene was upregulated 2.16-fold in patients with HIVLD than in patients without HIVLD. In conclusion,MTP-493C/T polymorphism influences the expression level ofMTPin patients without HIVLD. Individuals without HIVLD havingABCG234GA genotype with impaired triglyceride levels may facilitate dyslipidemia risk.