BACKGROUND Melatonin, with its antioxidant properties, plays a pertinent role in influencing the pathogenesis of periodontal disease. This study aims to detect the presence of melatonin in gingival crevicular fluid (GCF) and to assess the levels of salivary and GCF melatonin in periodontal disease and show the correlation between salivary and GCF melatonin. METHODS Forty-five subjects, based on the gingival and Russell periodontal indexes, were grouped as 15 healthy subjects (group 1), 15 subjects with gingivitis (group 2), and 15 subjects with periodontitis (group 3). Saliva and GCF samples were collected from all subjects. Melatonin levels were assessed using an enzyme-linked immunosorbent assay. The paired-sample test was used to correlate between saliva and GCF. RESULTS Melatonin was present in GCF (mean: 1.54 pg/ml) with significantly less concentration compared to that of saliva (mean: 2.17 pg/ml). Salivary and GCF melatonin levels were reduced to the lowest concentrations in patients with chronic periodontitis (salivary melatonin: 0.07 pg/ml; GCF melatonin: 0.06 pg/ml; P <0.05), which were inversely proportional to the clinical indices. There was no significant correlation between salivary and GCF melatonin levels (P >0.05). CONCLUSIONS Melatonin was expressed in GCF. Salivary and GCF melatonin levels varied from clinically healthy subjects (group 1) to subjects with periodontitis (group 3). Both salivary and GCF melatonin levels decreased in group 3 subjects compared to group 1 subjects, indicating that melatonin may have a protective role against periodontal disease, although further research is required to validate this hypothesis.