Determination of the human lymphocyte subpopulation selected by immunofluorescence and the phenotypic analysis of hematological malignant cells by laser flow cytometry have become popular and useful tests in various laboratories. However, several lines of evidence have questioned the accuracy and reproducibility of these analysis. We examined the problems of laser flow cytometric analysis to measure the lymphocyte subpopulation and determine the phenotypic expression of hematological malignancies. In lymphocyte subset analysis, no survey has been applied to reveal the accuracy and reproducibility of these tests. We compared the accuracy of gating events and the ratio of lymphocytes using leuco GATE/simul SET analysis to those by manual gate method analysis. We found that there were some patients with SLE in which the accurate lymphocyte subpopulation was difficult to calculate due to the gating of lymphocytes by either method. Furthermore, apparent differences in the lymphocyte population were observed between these methods. In the phenotypic analysis of hematological malignancies, there have been several problems over 30% of the total cells had to be abnormal cells. Second, the malignant cells were difficult to gate unless the information of the size, shape and cellular density were obvious. Third, the phenotype of malignant cells were often different from that of the normal matured cells in the some lineage. However, flow cytometric analysis was useful to determine the cell lineage of peroxidase-negative cells and to diagnose the hybrid leukemia. In summary, the phenotypic analysis using flow cytometry and various monoclonal antibodies are clinically useful tests to diagnose the immunological disorders and hematological malignancies. However, there remain several problems to be solved in the near future.