Mitochondrial DNA (mtDNA) deletion affecting 4977 base pairs (mtDNA4977), the most common mtDNA mutation in humans, was analysed in brain specimens (frontal, temporal, and cerebellar cortices, caudate nucleus, thalamus, and hippocampus) and in other tissues (blood clot, liver, kidney, heart, and muscle) taken at autopsy of deceased neonates. mtDNA4977 deletion determined by polymerase chain reaction (PCR) could be demonstrated in each neonatal sample, however, quantity of mtDNA4977 deletion was less in the newborn samples than in those of the elderlies. Results obtained suggest that contrary to certain data mtDNA4977 deletion can be present in neonates. The mtDNA4977 deletion could be generated by perinatal hypoxia or temporary oxygen oversaturations during the intensive care of the neonates, as the mtDNA is sensitive to oxidative damage. In combination with other factors an additional causative role of mtDNA4977 deletion reported here cannot be ruled out in development of cerebral palsy or mental retardation of unknown origin often seen in neonates underwent neonatal intensive care procedures.