The objectives of this study were to determine arginine and glutamate levels in the gingival crevicular fluid (GCF) of adult chronic periodontitis patients versus periodontally healthy controls, and to compare two kinds of microdialysis probes: normal and U-shaped probes. The analysis of GCF components was developed to improve the diagnosis of periodontal disease (PD). Proteolysis in the periodontal tissues increases the concentration of amino acids (aa) in the GCF and the levels of these aa may reveal PD features and stages. GCF samples were collected by microdialysis in situ from 5 periodontally affected sites (probing depth 5 mm, clinical attachment loss 3 mm) in 14 adult chronic periodontitis patients and from 14 adult periodontally healthy controls. Capillary zone electrophoresis coupled to laser induced fluorescence detection was used to measure concentration of arginine and glutamate in the GCF. Data were analyzed statistically by ANOVA and Tukey's post-hoc tests (á=0.05). Arginine concentration was increased (p<0.001) and glutamate concentration was decreased (p<0.001) in chronic periodontitis patients as compared to controls. There were no significant differences (p=0.069) between the normal and U-shaped probes. In conclusion, the increase of arginine and decrease of glutamate concentration in GCF were associated to the presence of periodontitis, and might be used as markers to recognize periodontally susceptible subjects as well as to evaluate the treatment course.