Coronary Heart Disease (CHD) is the most common type of Cardiovascular Disease (CVD). CHD is influenced by various genetic and environmental factors. A number of risk factors such as dyslipidemia, obesity, oxidative stress, smoking and hypertension have been associated with the disease. Dyslipidemia has been marked to play an integral role in the development of CHD. Polymorphism of the apolipoprotein E (apo E) gene may influence lipid metabolism by modulating lipid levels in the circulation. The apo E polymorphism has been considered as one of the important risk factors for CHD. The most common alleles of apo E are ε2, ε3 and ε4 which make six genotypes. The current research work has been designed to determine the relationship of apo E with lipid levels in patients of CHD. A case control study was carried out with equal number (n=110) of normal human subjects and CHD patients. DNA was extracted from the blood samples which were collected after taking informed consent from the participants. Genotyping was performed by Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR- RFLP) at Single Nucleotide Polymorphisms (SNPs) rs429358 (ApoE4) and rs7412 (ApoE2). The genotype percentages were: E3/E3 (75%), E2/E3 (4.1%), E3/E4 (20%), E4/E4 (0%), E2/E4 (0%), and E2/E2 (0.45%). The allele frequencies were 0.025, 0.875 and 0.1 for ε2, ε3 and ε4, respectively. In control group allele frequencies for ε2, ε3 and ε4 were 0.045, 0.83 and 0.127, respectively, whereas in patients group allele frequencies for ε2, ε3 and ε4 were 0.045, 0.682 and 0.273 respectively. After performing ANOVA, total cholesterol (TC), low density lipoprotein cholesterol (LDL-C) and triglyceride (TG) levels were significantly high in patients group as compared to controls (p<0.001). High density lipoprotein cholesterol (HDL-C) level was high in controls than in patients group (p<0.05). Carriers of ε4 allele revealed high levels of TC and LDL-C levels (p<0.001) whereas ε2 allele carriers showed elevated levels of HDL-C (p<0.05) indicating protective effect of ε2 allele. Frequency of ε4 allele was found to be high in patients group when compared with controls indicating a relationship of ε4 allele in apo E gene with dyslipidemia Thus apo E polymorphism has a significant influence on lipid profile of an individual.