Periodontitis leads to immunologically mediated loss of periodontium and, if untreated, can result in tooth loss. Periodontal diseases are the most prevalent in the world and have a very strong impact on patients’ well-being and general health. Their treatment generates enormous costs. Given the above, precise, prompt, and predictive diagnosis of periodontal disease is of paramount importance for clinicians. The aim of the study was to summarize the state-of-the-art knowledge of molecular periodontal diagnostics and the utility of its clinical application. There is a great need to have diagnostic tests that not only describe the periodontal destruction that has occurred in the tissues but also allow clinicians to detect disease at a subclinical level before the changes occur. A test that would enable clinicians to follow the course of the disease and detect areas prone to exacerbation could be used to evaluate the effectiveness of ongoing periodontal therapies. Unfortunately, there is no such diagnostic method yet. A hopeful prospect is molecular diagnostics. There are numerous studies on biomarkers of periodontal disease. Point-of-care tests are also emerging. There are possibilities for processing large biological datasets (omics data). However, all of the above have a minor role in the overall single-patient diagnostics process. Despite advances in microbiological, molecular, and genetic research, the basis of periodontal diagnosis is still clinical examination enriched by the evaluation of radiological images.