Neutropenia is usually detected shortly after birth, affecting 6% to 8% of all newborns in neonatal intensive care units (NICUs). Out of the approximately 600,000 neonates annually treated in NICUs in the United States, 48,000 may be diagnosed as neutropenic. The incidence of neutropenia is greater in premature infants. Six to fifty-eight percent of preterm neonates are diagnosed with this auto-immune disease. The incidence of neutropenia correlates with decreasing birth weight. The disorder is seen up to 38% in infants that weigh less than 1000g, 13% in infants weighing less than 2500g, and 3% of term infants weighing more than 2500 g. Neutropenia is often temporary, affecting most newborns in only first few days after birth. In others, it becomes more severe and chronic indicating a deficiency in innate immunity.

The pathophysiology of neutropenia can be divided into "congenital" and "acquired". In congenital neutropenia (cyclic neutropenia) is autosomal dominant, mutations in the ELA2 gene (neutrophil elastase), is the genetic reason for this condition.

Acquired neutropenia (immune-associated neutropenia) is due to anti-neutrophil antibodies that work against neutrophil-specific antigens, ultimately altering neutrophil function.

Neutropenia fever can complicate the treatment of cancers. Observations of pediatric patients have noted that fungal infections are more likely to develop in patients with neutropenia. Mortality increases during cancer treatments if neutropenia is also present.

Congenital neutropenia is determined by blood neutrophil counts (absolute neutrophil counts or ANC) < 0.5 × 10/L and recurrent bacterial infections beginning very early in childhood.

Congenital neutropenia is related to alloimmunization, sepsis, maternal hypertension, twin-to-twin transfusion syndrome, and Rh hemolytic disease.