Endocrine diseases are rare and can present very subtly in the neonatal period. Most are diagnosed using newborn screening in the United States; however, some infants may present with false negatives or more subtle findings. Endocrine etiologies should be considered during the management of critically ill infants. This article will give an overview of endocrine emergencies encountered in the neonatal period, including disorders of glucose metabolism, thyroid disorders, adrenal disorders, and pituitary disorders.