Background: Significantly improvements in the medical science and advanced in medical equipment and hospital facilities have increased the survival rate of poor prognosis infants (PPIs), including premature/extremely low birth weight, asphyxiated, and born with potentially lethal congenital disorders. However, availability of medical resources was not at the same levels across Iran’s cities. Thus, the country health care system encounters to a challenging question about providing advanced care to PPIs. Methods: The present study aimed to develop a national guideline for management of PPIs. We reviewed 120 articles, protocols, and guidelines, and held 15 sessions with 42 active participants. Semi-structured interviews were performed separately with medical specialist teams, medical ethicists, religious masters (Shia clerics), and parents of PPIs. Results & Conclusions: This guideline is the first nationwide attempt to prepare a comprehensive framework that can support prenatal counseling in Iranian hospitals with various medical facilities to achieve more homogeneity in newborn medical care. In addition, we collected an extensive list of lethal congenital malformations, genetic disorders, inborn errors of metabolism and covers the main areas of concern with a clearly states of responsibilities for decision-making regarding prenatal counseling for PPIs across Iran.