Background: Biomarkers of oxidative stress can be measured in saliva and represent a promising tool for the research of oral diseases. Saliva sampling and further processing has been improved by Salivette collection systems. The aim of this study was to analyze the effects of two different Salivette collection systems on salivary biomarkers of oxidative stress in comparison to whole unstimulated saliva. Methods: Whole unstimulated saliva and saliva samples collected using cotton and polypropylene Salivette collection systems were obtained from 20 young healthy volunteers (aged 20-30 years). Advanced glycation end products (AGEs), advanced oxidation protein products (AOPP), thiobarbituric acid reacting substances (TBARS), ferric reducing ability of saliva and total antioxidant capacity were measured. Results: In samples collected using the cotton Salivette, higher AGEs and TBARS concentrations (by 97% and 2036%) were determined. In samples collected using the polypropylene Salivette cortisol, cortisol AOPP concentrations were lower (by 60%) in comparison to measurements in whole unstimulated saliva. Markers of antioxidant status were comparable in all types of samples. Conclusions: Salivette and Salivette cortisol collection systems significantly altered the determined concentrations of several markers of oxidative stress in comparison to measurements in whole unstimulated saliva samples.