Apolipoprotein E (apo E) modulates the metabolism of atherogenic lipoprotein particles and participates in the process of cellular incorporation of specific lipoproteins. Genetic polymorphism of apo E has been reported as an important dyslipidemia genetic marker associated with coronary artery disease. Type 2 diabetes mellitus is a disease with a high incidence and prevalence in the world. The main cause of death in these patients is myocardial stroke and a high incidence of general cardiovascular complications. The purpose of this work was to characterize the genotype of apo E in diabetic patients from Talca, Chile, in order to describe the allelic frequency of the apo E gene and its correlation to the lipids profile. Type 2 diabetic patients (200) were recruited from the Diabetes Program of Talca Hospital, Chile. Apo E genotype was determined by restriction fragment-length polymorphism analysis. A biochemical characterization was performed in all the subjects. Type 2 diabetic patients had elevated levels of glycemia, lipid profile and BMI compared to the control group. The E3/3 genotype and epsilon3 allele had a higher frequency in both groups. The E2/3 and E3/4 genotypes had higher levels of triglyceride (TG) and cholesterol respectively; however, there was not any statistical relationship between them. In conclusion, genotype of apo E in diabetic patients did not differ with healthy; E2/3 and E3/4 genotypes tend to have higher levels of triglyceride and cholesterol respectively. We think that these results corroborate that in the etiology of the dyslipidemia, there is more than one associate genetic marker.