Behcet's Disease (BD) is a rare, autoimmune, chronic and inflammatory disorder whose cause is not fully understood. This study was aimed to determine apolipoprotein E gene (APOE) polymorphism, and its relationship with serum lipid levels in BD. The study group consisted of 30 BD patients (18 male, 12 female) and 51 healthy volunteers (29 male, 22 female). Levels of serum lipids were determined by enzymatic, and apolipoproteins by the immunonephelometric methods. Genetic analysis of the APOEpolymorphism was carrried out using the polymerase chain reaction (PCR)-based assay. Although the levels of total and low density lipoprotein cholesterol (TC and LDL-C respetively), apolipoprotein B (APOB) and erythrocyte sedimentation rate (ESR) had significantly (p< 0.05) higher in patients than healthy volunteers, the levels of APOA-I, APOE, triglyceride (TG), high density lipoprotein cholesterol (HDLC), polymorphonuclear leukocytes (PMNL) and frequencies of APOE alleles were not significantly different in both healthy and in patient groups. In conclusion, APOE gene polymorphism could not show a distinctive feature in BD patients.