Objectives: The aim of this study was to evaluate the effect of non-surgical periodontal therapy on salivary melatonin levels in patients with chronic periodontitis. Materials and methods: Thirty individuals were included in this study.  Fifteen individuals with severe generalized chronic periodontitis as a study group and other fifteen individuals with healthy periodontium as a control group.  Clinical periodontal parameters (plaque index, gingival index ,bleeding on probing ,periodontal pocket depth and clinical attachment level) were recorded at baseline for both groups (study and control) and four weeks after nonsurgical periodontal therapy for the study group.  Stimulated saliva samples were collected from the study group at baseline and four weeks after SRP and taken from the control group only once.  The patients were treated by meticulous scaling and root planning .The samples were analyzed using ELISA method.   Results: After SRP all clinical periodontal parameters of the study group showed significant reduction (p < 0.001) when compared to their values in the baseline. At baseline, periodontitis patients showed significant decreased salivary melatonin level (p < 0.001) when compared to the control group.  Non-surgical periodontal therapy resulted in a recovery of the decreased salivary melatonin levels in chronic periodontitis patients as the mean value of salivary melatonin level after SRP was  significantly increased when compared to its level at the baseline (p < 0.001) however it did not reach the level of the control group and there was still significant difference (p < 0.001). Conclusion:Melatonin was decreased in saliva of severe generalized chronic periodontitis patients when compared to healthy individuals. Salivary melatonin levels recovered after periodontal therapy. This may imply the local involvement of melatonin in the pathogenesis of   periodontitis due to its antioxidant abilities. Salivary melatonin could be used as risk indicator for the severity of periodontal disease.