Periodontal diseases range from the relatively benign form of the disease known as gingivitis, to the chronic and aggressive periodontitis, which are not only a threat to the dentition, but also a threat to the overall health. During the last decade the search for the biomarkers of periodontal diseases becomes more and more interesting. We are looking for specific biomarkers that would be important for the diagnosis, prognosis and monitoring of diseases, but also for the patient's response to the therapy. Proteomic analyses have been increasingly used in the identification of proteins in patients with periodontal diseases, and have also found their place in the research dealing with the detection of possible biomarkers. Proteins are a potentially large source of biomarkers since they are the molecules that connect the static genome of the individual and the biological activity of the organism. Results of the proteomic studies of periodontal diseases show a wide range of proteins that could contribute to the better understanding of pathological changes that occur during disease. Among the most interesting proteins stand the annexins, S-100 and 14-3-3 proteins, lipoproteins and matrix metalloproteinase. In addition to these proteins, according to their function and behaviour, there are also many other interesting names, but the problem is the same. Further research with a larger number of samples is required for the possible designation of biomarkers of periodontal diseases.