Background: Salivary stress-related biomarkers in connection with periodontal disease have not been extensively studied. In addition to cortisol as a well-known marker of stress loading, chromogranin A (CgA) and α-amylase (AA) are supposed to link the activity of the neuroendocrine system to local and systemic immune functions and to be related to periodontitis. This study aims to determine CgA and AA in saliva and serum in periodontal health and disease to assess their potential relationship to periodontitis. Methods: Patients with aggressive (AgP) (n = 24) and chronic periodontitis (CP) (n = 34) as well as healthy control (CO) (n = 30) individuals participated in this study. CgA and AA were determined in saliva and serum with enzyme-linked immunosorbent assay and an adapted clinical amylase test; salivary cortisol was determined using mass spectrometry. Clinical parameters of periodontal disease were evaluated, and their possible correlations with stress-related biomarkers were assessed. Results: Significantly higher CgA levels were found in the saliva of patients with AgP compared with those in patients with CP and CO individuals (P <0.001). Salivary cortisol levels were higher in the AgP group compared with those in patients with CP (P <0.05). No differences in serum CgA levels and salivary and serum AA activities were found among all groups. A positive correlation was revealed between salivary AA activity or salivary CgA levels and the extent of periodontitis (P <0.05). Conclusion: The results suggest an association of CgA and cortisol levels as well as AA activity in saliva with periodontitis, especially a significant relationship of salivary CgA and cortisol to AgP.