Alloimmune neonatal neutropenia (ANN) is a rare but potentially life-threatening disorder of neonates. Demonstration of alloantibodies against granulocyte-specific antigens shared by neonatal and paternal granulocytes in the maternal serum is essential in the diagnosis of ANN. In contrast to granulocyte-specific alloantibodies, the significance of human leucocyte antigen (HLA) class I antibodies for ANN is still a matter of debate. We report on a case of severe isolated and prolonged neutropenia due to anti-HLA B49 alloimmunization only. Immediately after birth, severe, isolated neutropenia was observed and lasted for up to 2 months. Results of serologic testing showed only anti-HLA B49 antibodies in the maternal and neonate's sera. HLA typing showed HLA class I (B49) incompatibility between the mother and the child. Granulocyte-specific antibodies were not detected. Adsorption of the maternal serum with HLA B49-bearing platelets removed serum reactivity with paternal neutrophils. Our results support the idea that certain HLA class I antibodies can induce ANN.