In the northern West Bank, 14-year-old Salah al-Din Abu Muhsin was shot as he played with a toy gun he had been given as a present for the Eid holiday, witnesses and medical sources said.
Relatives of the boy said on Thursday that he was with a group of children and youths throwing rocks at the soldiers when he raised a homemade toy gun put together from metal scraps and aimed it at the troops.
A soldier shot the boy, they said, and he was pronounced dead at the hospital in the nearby town of Jenin. An Aljazeera correspondent reported he had been shot in the back.
Confrontations erupted after Israeli military patrols raided the town in the morning, Aljazeera's correspondent said.
The Israeli military said a large crowd of people had gathered and were beginning to riot when troops spotted what appeared to be an armed man in the crowd and fired.
Several hours later, a 13-year old Palestinian boy was shot dead in the southern Gaza town of Rafah, while walking with his family during the Eid festival, medics said.
Salah Abu al-Aish was hit in the neck as they passed near the entrance to Rafah's sprawling refugee camp.
The sources said it was not clear why the soldiers opened fire.
An Israeli army spokesman said soldiers opened fire when they spotted two Palestinians crawling very close to the Tarmit army outpost.
The two deaths raised the overall toll since the September 2000 start of the Palestinian uprising to 4713, including 3659 Palestinians and 980 Israelis.
Meanwhile, fighters of the armed resistance group, al-Aqsa Martyrs Brigades, claimed to have killed a suspected Palestinian collaborator in the West Bank.
The 45-year-old man died in a hail of gunfire on a street near Jenin.