The Shanidar 5 remains were found during the 1960 excavations, in layer D, about 4.5 meters below datum. He was an adult Neanderthal, thought to be male and around 40–50 years of age before death. He was caught in the same rockfall that killed Shanidar 1. Recovered were a cranium, 4 teeth, 1 vertebrae, 8 ribs, and miscellaneous other bones. The arrangement of the broken skeletal remains was thought to have been due to animals intervening after death. Radiocarbon results put the date at about 46,000 before the present day. Some years later a small correction to the original cranial reconstruction was found. During the recent excavations, more pieces of Shanidar 5 were found.

The cranium of Shanidar 5 was reconstructed by Erik Trinkaus and his colleagues beginning in 1976 and was finalized in 1994 after correcting a couple of errors in the process. During the process of reconstruction, there were discussions suggesting signs of intentional cranial deformation. Erik Trinkaus suggested that Shanidar 5 had its cranium deformed intentionally as an infant. However, this implication was overruled since the curve was missing after the correction of a misplaced cranium bone fragment. Still, the frontal mid-sagittal angle of this individual was very flat at 147º. The cranium shows signs of endocranial hyperostosis where plaques are found in the left and right side of the frontal crest and the front area of the sagittal sinus.