Background & Aims: Lipoprotein lipase (LPL) is one of the key enzymes regulating the metabolism of triglycerides (TG) and HDL cholesterol. The lipoprotein lipase (LPL) gene polymorphisms are possibly involved in the pathophysiology of dyslipidemia. Hind III polymorphism is one of the most common polymorphisms in LPL gene. In some studies, association of Hind III polymorphism with dyslipidemia has been reported. Due to the high incidence of dyslipidemia in Iranian adults, this study was designed to investigate the frequency of rare allele (H- ) LPL gene Hind III polymorphism and its association with serum lipids levels in an Iranian population, Methods: Total genomic DNA was prepared from 76 Iranian patients with hyperlipidemia [ Total cholesterol (TC) > 200 mg/dl, Triglyceride (TG) > 150 mg/dl] and 75 healthy subjects (TC < 200 mg/dl, TG < 150). The Hind III polymorphism was analyzed by polymerase chain reaction and restriction fragment length polymorphism. Results: The frequencies of the Hind III polymorphism minor allele (H- ) were 17 and 30 in the case and control groups respectively (P<0.01). In the case group, patients with H+H + genotype had significantly higher mean total cholesterol (TC) and low density lipoprotein (LDL), compared to those with H+H - and H-H - genotypes (P< 0.05). Conclusion: The presence of rare H+ allele was associated with increased TC and LDL-c levels in the studied population. The association between the LPL gene Hind III polymorphism and dyslipidemia is quite complicated and genotyping of LPL Hind III polymorphism in a larger-scale screening and with other polymorphisms is necessary and justifiable