Aim of the study: detect single nucleotide polymorphisms in cyclooxygenase-2 gene at -1195G/A and -765G/C , determine the frequency of polymorphisms in Egyptian population with chronic periodontitis and aggressive periodontitis and evaluate the effect of single nucleotide polymorphisms of the cyclooxygenase-2 gene on the clinical picture and treatment outcome of chronic periodontitis and aggressive periodontitis.Material and methods: The study included a total of 50 individuals that were divided into 3 groups; HC group with clinically healthy periodontium, diseased control group suffering from CP and patients' group suffering from AP. Patients and healthy controls received a full-mouth periodontal examination which included gingival index, periodontal probing depth, and clinical attachment level. The clinical diagnosis was confirmed by taking full-mouth periapical radiographs. Patients were divided into two groups; group I A.P patients and group II C.P patients, both were treated nonsurgical with follow up (baseline, 1 month, 2 months and 3 months). Venous blood was taken by standard venipuncture and placed into sterile EDTA-containing tube for DNA extraction and amplification by RFLP-PCR technique. The resulting fragments were separated by agarose gel electrophoresis and visualized by ethidium bromide staining and UV light.Results: The results of the present study showed that there was no statistically significant difference between distribution of the different genotypes as well as the different alleles at ─1195G/A and at ─765G/C in the three groups; CP, AP and healthy control. The A allele in ─1195G/A represented highest frequency in AP group followed by CP and control groups, without statistical significance. As regards for ─ 765G/C the G allele was more frequent in the AP than in the CP and control groups. Regarding the clinical parameters results, CAL and PPD decreased through the whole study; baseline to 3 months; in both CP group, where it was statistically significant, and AP group where there was no statistical significance. GI and PI decreased in both groups with statistical significance. There was no statistically significant association between clinical parameters and different genotypes at ─1195G/A or at ─765G/C in CP and AP both groups. Conclusions: Although our results were found not statistically significant, it suggests that COX2 gene polymorphism might play an essential role in the periodontal destruction and bone resorption in both types of periodontitis.