Flow cytometry (FCM) is the measurement of numerous cell properties as the cells move in single file in a fluid stream and interrupt a beam of laser light. The use of FCM in clinical laboratory has grown substantially in the past decade. In hematology it can be used for leukemias and lymphomas phenotyping. Its important role is in the detection of minor haematopoietic populations, this role is extremely obvious in detection of minimal residual disease (MRD), identification of prognostically important subgroups, haemopoietic progenitor cell enumeration and reticulocyte enumeration. It can also be used for diagnosis of paroxysmal nocturnal haemoglobinuria (PNH). Our aim is to highlight the strategy of flow cytometry in picking up the different minor hematopoietic populations depending on their own known characteristics. This helps to optimize subsequent treatment strategies, and will benefit the individual patient.