Flow cytometry is a potent tool to dissect the phenotypes and functions of cell subsets by measuring multiple parameters on a single-cell basis. However, intracellular staining may be time consuming and more steps, particularly in cytokines, could be problematic for its use in daily routine or in large cohort testing. Lately, a novel reagent has been developed to perform intracellular staining in one step. The objective of our study was thus to assess this new method in comparison with the reference technique by focusing on CD4+ T-cell subsets such as Th1, Th2, and Th17 cells in clinical samples. Peripheral blood was collected from 10 children with aplastic anemia and 10 healthy volunteers and stained using the reference and one-step methods. Different subsets of CD4+ T-cells, which are defined as Th1, Th2 and Th17 cells, were investigated by flow cytometry. The repetitive experiment was designed to study intraassay precision. Correlations were studied using Pearson's correlation coefficient test. When comparing results obtained with the two techniques, no statistical differences between the percentages of Th1, Th2, and Th17 cells were observed. Besides, a nice correlation between percentages of Th1 cells obtained with the two different methods was identified in the global population (r: 0.777, p < 0.01). Likewise, percentages of Th2 cells (r: 0.875, p < 0.01), and Th17 cells (r: 0.886, p < 0.01) were strongly correlated between reference and one-step procedures. Importantly, flow cytometry staining obtained with the one-step method was very robust with a nice intra-assay precision and a better discriminative power and repeatability. With better staining quality and a shorter realization time, one-step intracellular staining may provide an efficient way for daily routine testing of Th1, Th2 and Th17 cells, as well as for further research.