This paper provides guidelines to determine the differential diagnosis and treatment of sudden deterioration of an endotracheally intubated newborn infant. Since such an event is most often secondary to a mechanical problem, simple adjustment of the ventilator in response to blood gas analysis will only rarely be sufficient to stabilize the infant. The proposed algorithm integrates history, physical examination, investigations, and therapeutic intervention (of which manual ventilation is the keystone). We hope that such an algorithm may help training physicians, nurses, and respiratory therapists to minimize the risk for the infant as well as the time required to provide an efficient resuscitation. This algorithm may be used both in the neonatal intensive care unit and in the delivery room as a complement to the recommendations of the American Heart Association, in case of poor response to the resuscitation. Modifications to this protocol should be allowed according to specific characteristics of each infant and to the equipment available.