Hemophagocytic lymphohistiocytosis (HLH) may present with thrombocytopenia during the newborn period. Three neonates (one term and two preterm) presented during the newborn period with thrombocytopenia. Transient recovery occurred in two newborns. The diagnosis of HLH was made after the recurrence of thrombocytopenia and the clinical symptoms at 5 and 7 weeks. The third infant was a premature baby diagnosed at 8 days of age after manifesting the clinical and laboratory features of HLH. All three neonates were treated with chemotherapy and responded well. After hematologic and clinical remission was achieved, the two newborns received hematopoietic stem cell transplantation from allogeneic donors. The third neonate is currently receiving chemotherapy. Persistent or recurrent thrombocytopenia of undetermined cause during the neonatal period should raise the suspicion of HLH, even though other symptoms or signs are not yet evident.