The structure is underground, carved from limestone by hands that worked the Yucatán Peninsula’s bedrock centuries before anyone now living was born.

A chultún — the Maya term for a subterranean chamber, typically bottle-shaped or roughly cylindrical, dug into the porous rock beneath the surface — sits near one of the most studied archaeological sites in the Western Hemisphere.

Chichén Itzá, the great Classic and Terminal Classic Maya city that rose to regional dominance over the course of centuries and whose iconic stepped pyramid, El Castillo, draws more than a million visitors each year, is surrounded by a landscape that still yields new information about the people who built it.

This chultún was not a new discovery when researchers turned to it with the tools of ancient genomics.

The bones of children had been found there before, catalogued and studied by archaeologists using the methods their field had developed.

The burial had been interpreted as ritual in character, connected in some way to the religious life of a society that has attracted both genuine scholarship and significant misunderstanding in the centuries since Spanish colonizers first encountered Maya civilization.

What ancient DNA made possible in this context was a transformation in the quality and type of questions the evidence could answer.

Researchers generated genome-wide data from 64 subadult individuals whose skeletal remains had been recovered from the chultún.

The individuals came from a feature located near Chichén Itzá’s Sacred Cenote — the great natural well that served as a site of ritual significance and that has itself produced substantial evidence of past ceremony.

The analysis was published in the journal Nature in 2024, and its findings challenged assumptions, confirmed some existing interpretations, and opened new questions that the science alone cannot yet answer.

Within the first hours of reading the study, the headline finding is clear: all 64 analyzed individuals were genetically male.

Not some of them.

Not most of them.

Every single one of the children whose ancient DNA could be read was genetically male.

That finding, by itself, was remarkable.

Osteological sex estimation — determining the biological sex of an individual from skeletal remains — is reliable in adults, where the pelvis and other bones carry measurable differences between sexes.

In children, particularly young children, those differences are far less pronounced.

Juvenile skeletal remains are difficult to sex with confidence from bone morphology alone, and the children in this chultún appear to have been young — subadults rather than teenagers or adults.