Flow cytometry is a method that has been developed since 1950's and it has a pivitol role in clinical and research laboratories. Flow cytometry has been used in many scientific areas. Formerly this method was used in hematology laboratories, but at the present, it is used in clinical laboratories of hematology, immunology, oncology, microbiology, transplantation units, research laboratories, pathology, histology, and clinical biochemistry as both diagnostic and research tool. Besides clinical laboratories flow cytometry is widely used in reseaches in food, toxicology, and aquatic sciences. Deep knowledge of the principle flow cytometry method will help us to apply this method to different pathologies with outmost standardization and increase the diagnostic value.