Abstract: Objective　To analyze the role of paroxysmal nocturnal hemoglobinuria (PNH) clones in children with acquired aplastic anemia (AA). Methods　The relationship between the existence of PNH clones and clinical features in children with AA was retrospectively analyzed. The influence of PNH clones on the efficacy of combined immunosuppressive therapy (IST) of anti-thymocyte globuline (ATG) and cyclosporine A (CSA) was also observed. In addition, multiple factor analysis was used to analyze the main factors affecting the efficacy of AA. Results　One hundred and forty-eight children with AA were enrolled, including 74 cases (50%) of granulocyte PNH clones positive, 68 cases (45.9%) of monocyte PNH clones positive, and 93 cases (62.8%) of total PNH clones (granulocytes and / or monocytes) positive. In 49 children having both granulocytes and monocytes PNH clones, the clone size of monocytes and granulocytes was 0.7% (0.4%-1.5%) and 0.2% (0.1%-0.7%), respectively, and the difference was significant (P<0.001) and there was a significantly positive correlation between them (r=0.65, P<0.001). According to the different PNH positive clones (monocytes, granulocytes, total), children were divide into three groups. And there were no differences in gender, age, concurrent infection, white blood cell count, hemoglobin concentration, platelet count, neutrophil absolute count, reticulocyte percentage in different PNH clones positive and negative groups (P>0.05). The group with monocytes PNH clones positive had a positive effect on the efficacy of IST (P=0.02). Multiple factor logistic regression analysis showed that the concentrations of hemoglobin and the positive PNH clones of monocytes were the main factors affecting the efficacy (P<0.05). Conclusions　The high concentration of hemoglobin and the positive PNH clones of monocytes contribute the better effect of IST in children with AA.