Background: To date, flow cytometric immunophenotyping has not been used to investigate immune patterns in saliva samples from individuals with inflammatory processes in the oral cavity, such as chronic periodontitis (CP). Saliva analysis could be a non-invasive method for evaluating oral health. The objective of this study is to determine the phenotype of leukocytes and total immunoglobulin A (IgA), IgG, and IgM titers in the saliva of individuals with CP. Methods: Saliva samples were obtained from patients with CP (n = 12) and from a control group (n = 27) without oral diseases. Flow cytometry was performed to determine the frequency of T cells (CD4+ and CD8+), B cells, and natural killer (NK) cells as well as the total leukocyte population. Immunoglobulin titers were determined by dot enzyme-linked immunosorbent assay. Results: Cell immunophenotyping revealed that patients with CP had a higher frequency of total leukocytes (47.94% ± 5.1%; P < 0.001), B cells (43.93% ± 6.2%; P = 0.006), NK cells (0.16% ± 0.04%; P = 0.03), and CD4+ T cells (38.99% ± 4.4%; P = 0.002) than individuals without oral pathologies (24.75% ± 2.2%, 20.60% ± 2.7%, 0.09% ± 0.03%, and 16.82% ± 3.5%, respectively). No significant differences in salivary total IgA, IgG, and IgM titers were found between the two cohorts studied. Nevertheless, higher total IgG levels were observed in patients with CP, which could indicate a possible correlation between clinical attachment level and salivary IgG (P = 0.07; r2 = 0.08). Conclusion: These results show that cell phenotyping by flow cytometry could be an effective tool for determining leukocyte profiles in saliva samples from patients with CP and healthy individuals.