Currently, understanding the immune response, its abnormalities, and its diagnostic possibilities is a key point in the management of patients with various diseases, from infectious to oncological ones. The aim of this review was to analyze the data presented in the current literature on immune disorders and the possibility of their laboratory diagnostics in combination with clinical manifestations. We have performed a systematic analysis of the literature presented in international databases over the last ten years. We have presented data on the possibility of diagnosing immunopathological processes due to changes in immune cells and soluble molecules involved in the pathogenesis of a wide range of diseases, as well as the determination of antibodies to detect autoimmune processes. By applying laboratory techniques such as hematology, flow cytometry, ELISA, etc., available to most clinical laboratories worldwide, clinical data on immune system dysfunction in a wide range of diseases are being collected. This process is unfortunately still very far from being completed. However, with all the diversity of accumulated knowledge, we can currently state that the pathogenesis of the vast majority of immune-mediated diseases is not yet known. At the same time, the current success in dividing immune-mediated diseases into distinct clusters based on different types of inflammatory responses that are based on the involvement of different populations of T helper cells and cytokine molecules represents significant progress. Further research in this direction seems very promising, as it allows the identification of new target cells and target molecules for both improved diagnostics and targeted therapies.