Proteomic analyses enable large scale descriptions of protein expression in a variety of biological samples, and provide an advanced approach in proteome research. The aim of this study was to establish the changes in protein expression between the epithelial and connective periodontal tissues samples in healthy subjects (control group) and healthy sites, sites with gingivitis, periodontitis, and post treatment sites in patients suffering from generalized aggressive periodontitis (test groups). The study was conducted on eight patients divided into two groups. The test group consisted of four patients with generalized aggressive periodontitis (two male, two female), and the control group consisted of four subjects (two male, two female) with no signs of periodontal disease, referred to the Department of Periodontology for crown lengthening procedure. The epithelial and connective periodontal tissue samples in the test group were harvested during initial periodontal treatment, and in the control group during the surgical procedure. Tissue samples were stored in the RNAlater reagent according to the manufacturer’s instructions until further analyses. Proteins from tissue lysate were separated by 1D gel electrophoresis, in gel digested with trypsin, and measured by nano-scale HPLC system coupled to a mass spectrometer through a nano-electrospray ionization source. The obtained raw data was processed by MaxQuant software. A total number of proteins identified in the study was 3420. After statistical processing of data, a total of 193 proteins were identified and quantified in all samples, and showed statistically significant changes in expression level between the control group and test groups. Proteins that could possibly be a mark of periodontal health are: Multimerin-1, annexins, 14- 3-3 protein gamma; of gingivitis: Dedicator of cytokinesis protein 2, Band 3 anion transport protein; of parodontitis: Azurocidin, Myeloid cell nuclear differentiation antigen, histones, immunoglobulins, Prolargin; and of post treatment condition: Oligosaccharyltransferase complex subunit and Mimecan. The most interesting protein in the study was Azurocidin, showing the highest fold change in periodontitis and gingivitis. The results showed different protein expressions in tested groups and confirmed that proteomic analyses of periodontal tissue could contribute to a better understanding of the pathogenesis of periodontal diseases, and might even contribute to the improvements in diagnosis and prognosis of these diseases.