The aim of this study was to measure lipid peroxidation (as an end product of oxidative stress) and corresponding antioxidant activity in patients with periodontitis and assess the influence of smoking and periodontal treatment on these parameters. Thirty healthy subjects (including 15 smokers) were compared to periodontitis patients (n = 30, including 15 smokers). Malondialdehyde (MDA), glutathione peroxidase (GSHPx) and the total antioxidant capacity (TAOC) were recorded in saliva. The lowest level of lipid peroxidation (MDA) was measured in saliva in the non-smoking periodontally healthy subjects (0.065 +/- 0.05 micromol/l). MDA levels were significantly higher in periodontitis patients who smoked (0.123 +/- 0.08 micromol/l) compared to non-smoking controls (0.065 +/- 0.05 micromol/l; p < 0.05). The periodontally healthy subjects demonstrated significantly lower levels of GSHPx (antioxidative parameter) than the periodontitis group (p < 0.05). The TAOC flow rate (delivered antioxidant components within saliva) was significantly lower in patients with periodontitis (0.34 +/- 0.26 micromol/ml) in comparison to the controls (0.62 +/- 0.24 micromol/ml; p < 0.05). Patients with periodontitis demonstrate more lipid peroxidation than healthy subjects, and this effect is enhanced by smoking. Imbalance between oxidative stress and antioxidant capacity may play a role in the pathogenesis of periodontal disease. Non-surgical periodontal treatment leads to a reduction of MDA and GSHPx to levels comparable to healthy controls.