Objectives: Parafunctional habits, as one of the etiological factors of temporomandibular disorders (TMD), are an individual’s response to increased stress. During stress and depression, biomarkers such as cortisol and salivary alpha-amylase (SAA) are secreted in the saliva. The present study aimed to investigate whether there is a correlation between salivary stress biomarkers and parafunctional habits. Materials and Methods: Thirty-two cases, from May to September 2015, were selected based on two standard stress questionnaires, namely the depression anxiety stress Scale-21 (DASS-21) and the Beck Anxiety Inventory (BAI). Saliva samples were collected to examine the level of unstimulated salivary cortisol and SAA. The significance of the results was assessed via student’s t-test and Mann-Whitney test (α=0.05). Results: The mean concentrations of cortisol and SAA in unstimulated saliva were significantly higher in the case group than in the control group (P=0.01 and 0.44, respectively). The mean scores of anxiety, stress, and depression were significantly higher in the case group than in the control group (P<0.05). Conclusion: It seems that the levels of salivary cortisol and SAA, as well as stress, anxiety, and depression scores, are higher in patients with parafunctional habits.