A glass, marble, and bronze sarcophagus was built to hold the mummy, which was venerated by history buffs and churchgoers.
But in 1977, workers cleaning a crypt beneath the altar found two wooden boxes with human bones. One box held the remains of two children; an elderly female; an elderly male, complete; and an elderly male, headless; and some fragments of a sword. The other contained the lead box–inscribed as had been recorded in 1661–in which was a skull that matched postcranial bones of the headless man in the first box. A Peruvian historian, anthropologist, two radiologists, and two American anthropologists studied the remains. The man was a white male at least 60 years old (Pizarro’s exact age was unknown; he was said to be 63 or 65 by contemporary historians) and 5’5″ to 5’9″ in height. He had lost most of his upper molars and many lower incisors and molars, had arthritic lipping on his vertebrae, had fracture his right ulna while a child, and had suffered a broken nose.
Examination of the remains indicated that the assassins did a thorough job. There were four sword thrusts to neck, the sixth and twelfth thoracic vertebrae were nicked by sword thrusts, the arms and hands were wounded from warding off sword cuts (a cut on the right humerus and two on the left first metacarpal; the right fifth metacarpal was missing altogether), a sword blade had cut through the right zygomatic arch, a thrust penetrated the left eye socket, a rapier or dagger went through the neck into the base of skull, and a pair of thrusts had damage the left sphenoid. The savage overkill suggests revenge as a motive rather than simple murder or death in battle.
The scholars concluded that these were indeed the remains of Francisco Pizarro. The two children might be Pizarro’s sons who died young, the elderly female is possibly the wife of Alc ntara, and the other elderly male Alc ntara. The dried out body long thought to be Pizarro exhibited no sign of trauma as would be expected if it was indeed the corpse of the conquistador. They decided that the interloper was possibly a church official, and replaced the body with the conquistador’s bones in the glass sarcophagus.