The cave/grotto under the church has been venerated since the fifth century AD. According to tradition, the holy family stopped here during their flight into Egypt just prior to the slaughter of the innocents. This site is only 383 yards (350 meters) from the Church of the Nativity, so they had not gotten very far from Bethlehem. The tradition also states that while taking shelter in the cave a drop of Mary’s milk turned the cave’s stone to white (the cave is in chalk stone). Some Christians and Muslims believe that consuming crushed stone from the cave increases female fertility and quantity of a mother’s milk.
Regarding the ‘flight into Egypt’, the scripture report:
“behold, the angel of the Lord appeareth to Joseph in a dream, saying, Arise, and take the young child and his mother, and flee into Egypt, and be thou there until I bring thee word: for Herod will seek the young child to destroy him. When he arose, he took the young child and his mother by night, and departed into Egypt: And was there until the death of Herod [in 4 BC]: that it might be fulfilled which was spoken of the Lord by the prophet, saying, Out of Egypt have I called my son [prophecy found in Hosea 11:1].” Matthew 2:13-15.
The event of the ‘flight into Egypt’ occurs immediately after the wisemen depart from the holy family. According to scripture this happened sometime after Christ’s birth. He may have been as much as two years old (Matthew 2:16). As they returned from Egypt, it appears they intended to resettle in Bethlehem, but upon learning that Herod’s son, Herod Archelaus ruled over the region, the holy family moved to the safer country of Galilee, settling back at Nazareth. Herod Archelaus ruled Judea from Jerusalem only from 4 BC to 6 AD (10 years) but he was such a spectacularly bad ruler that Rome deposed him and made Judea a Roman province under Roman appointed governors (such as Pilate and Felix).
The scriptures do not tell us where in Egypt the holy family lived. Tradition holds that they were near Cairo, across the Nile River and the pyramids in Giza. At the time when the holy family were in Egypt, the great pyramids were already over 2,500 years old. Additionally, there was at that time a sizable Jewish population in Alexandria, Egypt, so that is another possible location.
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