The morphological characteristics of neurons and synaptic contacts in the neocortex following acute perinatal hypoxia and subsequent use of Saliphene were studied in later ontogeny (days 80–90) in 28 Wistar rats. Controls consisted of intact animals of the same age. Light and electron microscopy studies were performed, along with immunocytochemical detection of synaptophysin and morphometric studies. These investigations showed that hypoxia in the perinatal period leads to structural rearrangements in neocortical neurons in adult animals. Degeneration of some large pyramidal neurons in layer V was seen, with decreases in the density of synaptic contacts (almost twofold) in the deep layers of the neocortex. These impairments were probably due to modifications to the developmental program for structures and interneuronal contacts. The data obtained here provide evidence that the Russian formulation “Saliphene” has protective actions on neurons and their differentiation and synaptogenesis after hypoxia. This suggests that this formulation is clinically effective and provides grounds for continuing studies in this direction.