Background: The aim of this study was to investigate malondialdehyde (MDA), superoxide dismutase (SOD) and melatonin levels in the gingival crevicular fluid (GCF) of patients with chronic periodontitis (CP) and generalized aggressive periodontitis (GAgP) as biomarkers for oxidative stress. Methods: The study comprised 65 subjects: 15 healthy individuals, 25 CP patients and 25 GAgP patients. Plaque index, gingival index, pocket depth, clinical attachment level measurements and GCF samples were obtained from all subjects. MDA, SOD and melatonin levels were determined utilizing enzyme-linked immunosorbent assay. Results: GCF-MDA levels were significantly higher in the GAgP group compared to the CP and control groups (p < 0.001) and significantly higher in the CP group than the C group (p < 0.001). SOD and melatonin GCF levels were significantly higher in the control than the GAgP and CP groups (p < 0.05), and significantly lower in the GAgP than the CP group (p < 0.05). The CP group demonstrated a significant negative correlation between GCF-MDA and melatonin concentrations. A positive correlation was observed between SOD and CAL in the CP group and PD in the GAgP group. Conclusions: MDA, melatonin and SOD could be considered as biomarkers for oxidative stress in periodontal diseases and might be useful diagnostic aids in distinguishing CP and GAgP patients.