The  present  study  was  carried  out  on  eighteen  patients  having  aggressive  periodontitis (exhibiting at least three single-rooted teeth with periodontal pocket depth ≥ 5mm) divided into 3 groups, each group was six patients.   It was noticed that, surgical treatment of aggressive periodontitis was shown to be more effective than conventional scaling and root planing procedures alone. Additionally, the use of  antibiotic agent as adjunctive to surgical treatment was proven to be beneficial in the reduction or elimination of bacterial load in the tissues invaded the periodontopathogens. Among the known natural antibacterial agent, is the Propolis (bee glue) which also has many other pharmacological properties such as anti-inflammatory, and immune- modulatory properties. Therefore, the purpose of this study was to clinically evaluate the effect of Propolis in the treatment of aggressive periodontitis, and microbiologically test its effect against Actinobacillus actinomycetemcomitans. Clinical evaluation was performed using plaque, bleeding indices and PPD and CAL at baseline, six weeks and three months after surgical treatment for both groups (II), (III). The results revealed that there was statistical significant improvement in all clinical parameters for all patients after different methods of treatment. Microbiological, positive culture results were revealed in all samples collected before treatment, on the other hand, negative culture results were revealed in all samples collected six weeks after surgical treatment for both groups (II) & (III), as well as in all samples of group (III) collected after three months after treatment. Through this study we can concluded that systemic administration of propolis with SRP and periodontal flap surgery showed clinical and microbiological improvement reduction results in patients with aggressive periodontitis.