Considering the implications of B, T, and natural killer (NK) cells in the pathophysiology of systemic autoimmune diseases, the assessment of their distribution in the blood could be helpful for physicians in the complex process of determining a precise diagnosis. In primary Sjögren's syndrome, transitional and active naive B cells are increased and memory B cells are decreased compared to healthy controls and other systemic diseases. However, their utility to improve the accuracy of classification criteria has not been proven. In early untreated rheumatoid arthritis, proportions of regulatory T cells are constantly reduced, but other patterns are difficult to determine given the heterogeneity of published studies. In systemic lupus erythematosus, the lack of studies using large cohorts of patients and the diversity of the possible pathological mechanisms involved are also important impediments. Nevertheless, transitional B cell and plasma cell proportions are increased in most of the studies, the CD4/CD8 ratio is decreased, and the number of NK cells is reduced. Despite the low number of studies, anomalies of lymphocyte subset distribution was also described in ANCA-associated vasculitis, systemic scleroderma, and myositis. For now, flow cytometric analysis of lymphocyte subsets has focused mainly on specific subpopulations and is more useful for basic and translational research than for diagnostics in clinical practice. However, new modern methods such as mass cytometry and bioinformatics analyses may offer the possibility to simultaneously account for the relative proportions of multiple lymphocyte subsets and define a global profile in homogeneous groups of patients. The years to come will certainly incorporate such global lymphocyte profiling in reclassification of systemic autoimmune diseases.