Jenin's refugee camp: Scene of fierce fighting in April
The Israeli army said the aim of its latest operation was to arrest suspected militants.
Witnesses said there were heavy exchanges of gunfire as the troops entered the area, but there have been no reports of casualties.
Jenin suffered heavy casualties and extensive damage last month in the big Israeli offensive in the West Bank.
The military campaign was launched after a spate of Palestinian suicide bombings.
Israeli troops have continued to make brief incursions into Palestinian-controlled areas to arrest suspected militants.
Withdrawing
Arrests were made after the latest incursion on Friday morning, an army spokeswoman said.
Unconfirmed reports say a number of loud explosions were heard, possibly indicating the demolition of homes.
Israeli forces are said to have surrounded the house of a militant of the Islamic fundamentalist group Hamas and ordered him outside.
The militant, Jamal Abu al-Haija, did not appear, but his wife and children left the house, according to reports.
Soldiers then threw hand grenades inside and the house caught fire, the witnesses said.
The BBC's Michael Voss in Jerusalem reports that the Israelis are now withdrawing from Jenin following the overnight incursion.
Palestinian elections
Palestinians claim Israeli soldiers massacred civilians in a battle in Jenin refugee camp last month, an accusation Israel strongly denies.
Human rights groups say they have found no evidence of a massacre.
The campaigning group Human Rights Watch reports that at least 52 Palestinians died during the nine-day operation aimed at rooting out militants.
Twenty-three Israeli soldiers also died in the battle.
On Friday, it emerged that Palestinian leader Yasser Arafat had reportedly agreed to hold parliamentary and presidential elections within the next six months.
Mr Arafat decision follows intense American and European calls for reform within the Palestinian Authority, reports say.
It comes shortly after Palestinian legislators mounted their most high-profile challenge yet to the Palestinian leader.
They called for elections within a year and a new cabinet within 45 days.
Washington report
The US State Department has sent to Congress a report saying that in in the second half of 2001 it found no evidence that senior Palestinian officials were involved in planning or approving acts of violence on Israelis.
However, the report on compliance with the 1993 Oslo peace accords, indicated that senior leaders of the Palestinian Liberation Organisation and the Palestinian Authority knew about violence carried out by some militant groups against Israel, and did little to stop them.
It also said that those who had committed acts of terror were going unpunished.
The period covered ended before an incident earlier this year when Israel accused the Palestinian leader, Yasser Arafat, of knowing about attempts to deliver an arms shipment to Palestinian militants.