The boy, who was around 18 months old, appeared to have died of a skull fracture before his head was placed in a leather envelope, and then on a pillow in the 13th Century.
It was exhumed in 1998 and after more than a decade of research scientists have now identified neurons and cerebral cells that are still intact.
Frank Ruhli, head of the Swiss Mummy Project at the University of Zurich, Switzerland, said: “Although reduced by about 80 per cent of its original weight, it has retained its anatomical characteristics and, most of all, to a certain degree its cell structures.”
He said that the “unique case of naturally-occurring preservation of human brain tissue” would enable researchers to learn more about the robust nature of the brain and how it works.
Intriguingly, the brain was the only tissue preserved inside the child’s skeleton and was “almost intact”, said Mr Ruhli.
The gyri and sulci – grooves and furrows in layman’s terms – which make up the surface of the brain’s cerebral cortex were still visible, as well the frontal, temporal and occipital lobe, he added.
Even more amazingly, the cellular structure of the brain has largely been preserved.
Microscopic examination of the tissue revealed grey and white matter, blood vessels and large neurons near the hippocampus area, the memory-making region of the brain.
The research is published in the magazine Neuroimage.