There is high incidence of autism and Neanderthal anthropometry in the matrilineal and Dravidian language speaking nair community of Kerala. The autistic brain is comparable to the large-sized Neanderthal brain. Autistic metabolonomic patterns include low pyruvate dehydrogenase activity, mitochondrial dysfunction, GABA shunt, Warburg glycolytic phenotype, hyperammonemia, hyperhomocysteinemia, porphyria, low cholesterol/bile acid levels and a similar pattern is seen in the normal nair population of Kerala. Neanderthal metabolonomic patterns include a low efficiency PDH activity. Autistic and matrilineal societies like nair can be considered as remnants of the Neanderthals. The autistic and nair population have increased cytochromeF420 activity suggestive of endosymbiotic archaeal growth resulting in PDH and mitochondrial suppression. The increased archaeal growth in ice age conditions contributed to the neanderthal evolution. The autistic metabolonomic patterns are also seen in syndromeX, schizophrenia, cancer, multiple sclerosis and alzheimer’s disease suggesting neanderthalisation of the humans due to global warming and archaeal growth.