<p>Background: ATP-binding cassette transporter A1 (<em>ABCA1</em>) is a membrane integral protein which plays a vital role in High Density Lipoprotein (HDL) metabolism and exerts a protective effect against Hypoalphalipoproteinemia (HA) by mediation of rate-limiting step in HDL biogenesis. In addition, this protein possesses anti-inflammatory effects by inhibiting the production of some inflammatory cytokines in macrophages. This study investigated the association of <em>ABCA1</em>-565 C/T gene polymorphism with HA and serum lipids, IL-6 and CRP levels.<br /> Methods: A population which consisted of 101 HA and 95 normal subjects were genotyped for <em>ABCA1</em>-565C/T polymorphism by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). The serum concentrations of lipids, IL-6 and high sensitive-CRP (hs-CRP) were measured by the relevant methods.<br /> Results: The frequency of T allele was significantly higher in the HA group than the controls (31.7 <em>vs</em>. 19.5%, p=0.002). Thus, carriers of the T allele (CT and TT genotypes) had a higher risk for HA (p=0.016, OR=2.04, 95% CI=1.14-3.63). T allele carriers demonstrated decreased HDL-C and increased triglyceride, IL-6 and CRP levels than those with the CC genotype. &nbsp;<br /> Conclusion: This study suggests that the-565 C/T polymorphism of <em>ABCA1</em> gene is associated with an increased risk of HA, decreased HDL-C and increased TG, IL-6 and CRP.</p>