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The increasing importance of autoimmunity based diseases attracts the interest of pathologists, for whom the wide acceptance of indirect fluorescent antibody (IFA) technique at autoantibody screening is relevant diagnostic approach. The IFA method has gained perfection by introducing the so called diagnostic mosaics, consisting of various tissue sections (primate and/or mammalian in origin), of Hep-2 cells, of microbeads (biochips) coated with specific purified antigen(s) and/or of transfected HEK cells expressing the target autoantigens. As result of this, the IFA technique dominates not only in the detection of anti-nuclear antibodies (ANA) and of anti-neutrophil cytoplasmic antibodies (ANCA), but is useful also in the search for serological markers in many other autoimmune disorders. Among diseases in question, the inflammatory bowel disease (GAB, PAB, ASCA), celiac disease (ARA, AEmA, AGA) and/or autoimmune hepatitis (AMA, ASMA, ABCA, anti-LKM1, SLA/LP) have emerged as important. Furthermore, antibodies to gastric parietal cells (APCA), to skin epidermal structures (anti-BP180, anti-Dsg1, anti-Dsg3), antibodies against neurons (anti-Hu, anti -Yo) and glial cells (anti-AGNA) and to several endocrine gland cells (AICA, SCA, OAB, anti-TPO, anti-TG) have recently gained attention. In addition to ANA, the detection of autoantibodies against skeletal or cardiac striated muscles (ASMA/ACMA) is of prognostic value in systemic sclerosis, Sjoegren´s syndrome, dilated cardiomyopathy, myositis and dermatomyositis. At last but not least, detection of anti-sperm antibodies (ASA) has become important due to their association with infertility occurring in the absence of mechanical obstruction of female reproductive system. We bring here an overview of reasonable applications of IFA, which, in combination with additional immunological techniques such as immunoblot (IB), allows a precise identification of several autoantibody target proteins. Though this paper stresses the advantages of IB technique, the enzyme linked immunosorbent assay (ELISA) cannot be neglected, since it is inevitable for certain diagnostic decisions (Table 1).