White blood cells are produced in the bone marrow. They are released into the bloodstream, and travel wherever they are needed. Low levels of neutrophils occur when the bone marrow cannot replace them as fast as needed.
In babies, the most common cause is infection. A very severe infection may cause neutrophils to be used up quickly, and may also prevent the bone marrow from producing more neutrophils.
Sometimes, an infant who is not sick will have a low neutrophil count for no obvious reason. Some disorders in the pregnant mother, such as preeclampsia, can also lead to neutropenia in infants.
In rare cases, mothers may have antibodies against their baby's neutrophils. These antibodies cross the placenta before birth and cause the baby's cells to break down (alloimmune neutropenia). In other rare cases, a problem with the baby's bone marrow may lead to decreased white blood cell production.