The aim of this study was to investigate the involvement of the mesencephalic superior colliculus (SC) in the pathogenetic mechanism of SIDS, a syndrome frequently ascribed to arousal failure from sleep. We analyzed the brains of 44 infants who died suddenly within the first 7 months of life, among which were 26 infants with SIDS and 18 controls. In-depth neuropathological investigations of serial sections of the midbrain showed the SC layered cytoarchitectural organization already well known in animals, as made up of seven distinct layers, but so far never highlighted in humans, albeit with some differences. In 69% of SIDS cases but never in the controls, we observed alterations of the laminar arrangement of the SC deep layers (precisely, an increased number of polygonal cells invading the superficial layers and an increased presence of intensely stained myelinated fibers). Since it has been demonstrated in experimental studies that the deep layers of the SC exert motor control including that of the head, their developmental disorder could lead to the failure of newborns who are in a prone position to resume regular breathing by moving their heads in the sleep-arousal phase. The SC anomalies highlighted here represent a new step in understanding the pathogenetic process that leads to SIDS.