The aim of this study was to investigate association between of two MspI polymorphisms in ApoA-I gene (G-75A and C83T) and lipid profiles in Egyptian adolescent females with hypercholesterolemia and explore their effect on variations of lipid parameters. A total number of 120 adolescent females with hypercholesterolemia and 120 age matched normolipidemic healthy controls were enrolled for the study. Genotyping of the APOA1 was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) combined with gel electrophoresis, and then confirmed by direct sequencing. The frequencies of GA genotype were significantly lower in patients than in controls. Serum total cholesterol, low-density lipoprotein cholesterol and triglycerides were significantly higher and the HDL-cholesterol levels were significantly lower in subjects with GG genotype than those with GA + AA genotype. Moreover, the heterozygous CT and the T allele were significantly lower in patients than in controls. Carriers of T allele showed lower levels of cholesterol and triglycerides levels and the higher level of protective HDL than subjects with CC genotype. Significant association between GG/CC haplotype and increased lipid parameters was observed in patient group. In conclusion, both the G–75A and C83T polymorphisms of APOA1 gene have adverse effects on HDL levels and were associated with elevated lipid parameters. The study suggests that G and T alleles may be susceptible alleles for hypercholesterolaemia in Egyptian adolescent females and have a significant effect on lipid metabolism.