Causes of hypoxia and cyanosis in the term newborn can be found within all physiologic systems and take the form of hundreds of specific diagnoses. In the first and second parts of this series, a wide range of cardiac and pulmonary causes for newborn hypoxia and cyanosis have been examined. Because they are familiar, cardiac and pulmonary diagnoses often represent our reactionary opinions—the options that we first entertain even before a proper systematic approach to the infant has been taken. In this final of a three part series, neurologic, hematologic and metabolic disorders are explored as a cause for abnormal oxygenation, as well as sepsis and hypotension. It is within these final categories that we find many of the obscure possibilities for neonatal hypoxia—the diagnoses that often require rigorous testing, or more sophisticated laboratory interpretation. Without consideration of these elusive entities, however, appropriate treatment and referral will be unnecessarily delayed.