Neonatal alloimmune neutropenia (NIN) results from the destruction of foetal neutrophils by maternal immunoglobulin G-class neutrophil-reactive antibodies crossing the foeto-placental barrier. We report two cases of neonatal patients presenting with unspecific symptoms and persisting neutropenia accompanied by thrombocytosis. Both were subsequently diagnosed with NIN. These two cases of persisting neutropenia highlight the diversity of symptoms and the diagnostic challenges remaining in NIN. Furthermore, the cases remind us that neutropenia in neonates may be rooted in several different pathophysiological mechanisms.