One of the main etiological factors of the stomatognathic system dysfunction is stress and psychoemotional disorders. During stressful situations, there is an increase in the level of cortisol, the so-called stress hormone. Literature data indicate the existence of a correlation between blood cortisol levels and its amount in the saliva. This spurred an inspiration to undertake open, non-randomised studies, the objective of which was to conduct a comparative assessment of the saliva cortisol levels in patients with functional disorders of the masticatory system and in healthy volunteers, as well as to compare the results of cortisol levels with the results of survey-based tests with the use of Endler and Parker's CISS survey. Cortisol level was assessed due to its association with stress present in the body as one of the primary etiological factors of the stomatognathic system dysfunction, and hence the association of elevated cortisol levels assessed in the morning with the occurrence of dysfunctions of the stomatognathic system. The subject of the study is a group of 30 patients, of both sexes, aged between 20 and 46, who reported to the Dental Prosthetic Out-Patient Clinic of the Institute of Dentistry, Jagiellonian University in Cracow, for prosthetic treatment due to the painful form of functional masticatory organ disorders. The control group consisted of 30 subjects, aged between 19 and 41, in whom dysfunctions of the stomatognathic system were excluded. Collection of saliva for testing was performed at a fixed hour (9 am) into plastic test tubes with a stopper. Immediately after collection, the saliva was frozen at the temperature of -18 °C. The assessment of the cortisol levels was conducted by the high performance liquid chromatography (HPLC) with UV detection at the Department of Analytical Chemistry, Faculty of Pharmacy, Department of Laboratory Medicine of the Gdansk Medical University. Moreover, a 20-minute psychological test was conducted with the use of the CISS (coping inventory for stressful situations) survey in order to assess the patients in terms of their abilities to cope with stressful situations. The results obtained were submitted to a statistical analysis based on the conventional calculation procedures. The test group revealed significantly higher cortisol levels compared with the results obtained by the control group. The findings of the CISS survey confirmed the predominance of the emotion-focused strategy of coping with stressful situations in the test group. The results support the view that the psychoemotional factor is, to a considerable extent, conducive to the development of functional disorders. The elevated cortisol levels in patients with psychological disorders concur with the findings by other authors. The results obtained confirm that psychoemotional disorders may be one of the etiological factors of the stomatognathic system dysfunctions. The CISS survey, which was not used in similar studies before, makes it possible to obtain information on the subject's method of coping with stress, thus allowing for the initiation of a relevant psychological therapy aiding the prosthetic treatment.