Background Saliva has a powerful antioxidant activity proposing that it might have a protective role in the oral cavity. It is yet unclear, how circadian rhythm might affect this activity. Objective The main goal of this study was to compare the antioxidant status of saliva in patients with periodontal diseases (PD) to that of healthy people on a diurnal basis. Material and methods A total of 18 periodontal healthy individuals and 18 patients with chronic periodontitis were chosen. Samples of saliva were collected in the morning between 6:00 and 8:00 and in the evening between 6:00 and 8:00 (both stimulated and non-stimulated). The amount of glutathione (GSH), malondialdehyde (MDA), and total antioxidant status (TAS) in the salivary samples were analyzed, and its flow was also assessed. In addition, the scavenging capacity of saliva was tested in three systems generating oxygen free radicals. Results Results showed that GSH and TAS concentrations in the evening saliva of healthy subjects were significantly higher than those in the morning saliva, while MDA levels decreased (p<0.05). Conversely, there was no significant increase in GSH and TAS levels in the evening saliva of subjects with PD, and lipid peroxidation remained constant. On the other hand, the evening saliva of healthy subjects but not of subjects with PD was significantly more potent in scavenging free radicals in vitro than the morning saliva, especially for the superoxide (O2.-)radical (p<0.05). Moreover, scavenging activity was higher in stimulated than non-stimulated saliva. This activity was higher in evening saliva compared to the morning one and greater in healthy subjects compared to patients with PD (p<0.05). Conclusion A balance exists between oxidative stress and antioxidant mechanisms to maintain homeostasis in the oral cavity. This balance is deregulated in patients with PD as their saliva is unable to properly scavenge free radicals that might potentially increase over the day. Antioxidant supplements may be used in accordance with the circadian rhythm to minimize oxidative damage.