Aims The objective of this study was to investigate the association amongst the single nucleotide polymorphisms of genes encoding for matrix metalloproteinase (MMP) 1, 3, 9 and cyclooxygenase-2 (COX-2) of subjects. Protein production of MMPs, COX-2 and Vascular Endothelial Growth Factor (VEGF) were also investigated. Methods 280 chronic periodontitis patients and 250 periodontitis-free subjects were selected. DNA was extracted from blood samples of all patients, the polymorphic sites of the genes that encode for metalloproteinases and cyclooxygenase-2 were amplified using PCR, and digested with restriction enzymes. ELISA was used to determine the protein production of MMPs, COX-2 and VEGF. Results The mean probing depth (PD) was 5.4 mm and the clinical attachment loss (CAL) was 6.4 mm in patients group with at least 2 years history. 2G/2G genotype of MMP-1, the periodontitis patients presented frequency of 28% and the control only showed 3%. 5A/5A genotype of MMP-3, the periodontitis patients presented higher frequency of 55% than the control 40%. C/C of genotype MMP-9, the periodontitis patients presented higher frequency of 51% than the control 17%. C/C of genotype COX-2, the periodontitis patients demonstrated 28% frequency and the control was 3%. ELISA analysis determined a significant difference (p
