Animal scavenging, the pressure of sediment overlying the bones, the movement of water through the cave, root action, and countless other natural agents can produce damage to buried bones that superficially resembles injury or violence.

Distinguishing taphonomic from ante-mortem damage requires careful analysis of the specific characteristics of the damage — its location, the presence or absence of healing, the edge characteristics.

The third possibility is excavation damage — damage caused by the excavation itself in 1903, when Cheddar Man was removed from the sediment by workers whose methods were not as careful as modern excavation protocols would require.

Researchers have suggested that the skull damage may indicate a violent end, perhaps a blow to the head.