No shooting was heard as a column of around 20 vehicles, including trucks, drove into the West Bank town.
An Israeli army spokesman later said "our forces withdrew from Bethlehem after a brief, pinpointed operation".
On Friday, the occupation forces had entered Bethlehem for the first time since last summer before pulling out.
Israeli sources said some arrests had been made after troops entered the town in a column of armoured vehicles, without giving figures.
The raids followed a bombing on a crowded bus in Jerusalem on Thursday, where 10 people had been killed.
In the adjoining Ayda refugee camp, the occupation forces blew up the family home of policeman Ali Munir Yussef Jihar, who carried out the bus bombing near the residence of Israeli Prime Minister Ariel Sharon.
Bethlehem was one of the few places in the occupied West Bank from which the Israelis had withdrawn, handing it over last July to the Palestinian Authority.