Odontogenic cysts, are located in the jawbones, filled with fluid surrounded by epithelial lining and fibrous connective tissue. Vascular endothelial growth factor (VEGF) can induce physiological and pathological angiogenesis and is an endothelial cell-specific mitogen. The aim of the present study was to investigate whether any possible association between the VEGF insertion/deletion (I/D) variant and odontogenic cyst in Turkish population. Clinical information and venous blood samples were collected from 62 odontogenic cyst patients and 98 healthy controls. DNA was isolated from peripheral blood leukocytes. Genotyping of the VEGF I/D variant was done by the polymerase chain reaction (PCR) method. There was a statistically differece in terms of VEGF I/D allele frequencies between patients and controls. VEGF I/D variant I allele frequency was more prevalant in patients compared to controls (p = 0.006411, OR: 2.08, 95%Cl: 1.322-3.272). A statistically significant association was observed when the patients were compared with the controls according to D/D + I/D versus I/I genotype (p = 0.0508, OR: 1.925, 95%Cl: 0.872-4.246). The genotype distribution of VEGF I/D was not statistically different between patients and controls (p > 0.05). For the first time, our results provided evidence supporting the odontogenic cyst formation associated with the I/D variant at the promoter region of the VEGF gene in a group of Turkish population. Although it was seen in our study that the I/D variant in the promoter region of the VEGF gene supports odontogenic cyst formation, large-scale studies are needed to elucidate the effect of this variant on odontogenic cysts.