Aim To study apolipoprotein (apo) E polymorphism and its relationship with plasma lipids and apolipoproteins in Chinese patients with type Ⅱa hyperlipoproteinemia. Methods and Subjects Apo E genotype were assayed by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP), serum lipids were determined by enzyme method and apolipoproteins were measured by radial immunodiffusion assay in 87 type Ⅱa hyperlippoproteinemia patients whose fasting serum lipids levels were TG≤1.82 mmol/L,TC ≥6.21 mmol/L and 230 healthy subjects whose fasting serum lipids levels were TG≤1.82 mmol/L,TC<6.21 mmol/L from a population of Chinese Han nationality in Chengdu area. Results Compared with the control group the values of serum TG, TC, HDLC, LDLC, nHDLC, apo B100, apo CⅡ, apo CⅢ and apo E levels in patients with typeⅡa hyperlipoproteinemia were significantly increased (P<0.01) and the values of apo E/CⅢ ratio were significantly decreased (P<0.05). Apo E3/3 genotype and allele ε3 frequency in type Ⅱa hyperlipoproteinemia group and the control group were both the highest. Allele ε4 frequency in type Ⅱa hyperlipoproteinemia group was tended to increase than that in the control group and allele ε2 frequency was tended to decrease (P>0.05). In type Ⅱa hyperlipoproteinemia group the genotype of apo E₂ was with higher serum apo E levels compared with the genotype of apo E3, and the genotype of apo E4 was with lower serum apo E levels than those in genotypes E3 and E₂ (P<0.001). Conclusion Apo E gene polymorphism was associated with serum apo E levels in type Ⅱa hyperlipoproteinemia.