Diagnosis of autoimmune neutropenia (AIN) in infants is important, because it allows the exclusion of more severe forms of neutropenia that have an increased risk for leukemia. AIN is characterized by chronic neutropenia, which spontaneously resolves within several months to a few years, and mild infections. Diagnosis is confirmed by the presence of antibodies directed against neutrophil antigens. The human neutrophil antigen (HNA) system is a polymorphic system, which includes five antigen groups with different polymorphisms. In AIN, antibodies are mostly directed against HNA-1 (or against a specific allele of HNA-1) and HNA-4. Here, we present a series of 116 infants with AIN. We observed that anti-neutrophil antibodies were present in 60% cases; directed against HNA-1a in 73% of cases. In addition, we showed there was a bias in the HNA allele distribution in these infants because the frequency of the HNA-1a allele was greater in comparison with controls.