Background: Chronic benign neutropenia (CBN) and autoimmune neutropenia (AIN) are notoriously difficult to differentiate in children owing to their indistinguishable clinical course and varying availability and accuracy in the methods of anti-neutrophil antibody detection. This study aims to investigate whether the presence of anti-neutrophil antibody has implications on the disease course in Chinese children with AIN, as well as evaluating the various methods including LABScreen MULTI, granulocyte agglutination test (GAT) and granulocyte immunofluorescence test (GIFT) in anti-neutrophil antibody detection. Procedure: Chinese children under 18 years of age with neutropenia ≤ 1.5 x 109/L lasting 6 months or more in our single center were recruited into the study between 2016 to 2018. Patients with secondary causes of neutropenia were excluded. Blood for anti-neutrophil antibody and genotyping was taken once at the time of recruitment and subsequently when neutropenia recovered to ≥ 1.5 x 109/L. A combination of two in-house methods including GIFT, GAT and commercial kit LABScreenTM multipanel were used for the detection of antibodies. The age of onset, age of recovery, duration of neutropenia, gender, serial neutrophil counts, incidence of invasive infection, use of G-CSF were examined. Results: Using combined testing methods, anti-neutrophil antibody was detected in 30.8 % of patients and positivity was associated with more severe neutropenia, higher likelihood of infection and slower and later recovery compared to those without antibodies. Conclusions: The presence of anti-neutrophil antibody was useful in predicting the clinical course of patients with AIN. The use of combined testing methods increased the detection rate.