The Israeli air force bombed houses in Beit Lahiya and Khan Younis follows the firing of two rockets into southern Israel, Ynetnews.com reported.
The casualties were all in a house in Beit Lahiya, Palestinian officials said, describing the dead as members of Salah al-Din Brigades. An empty house in Khan Younis was gutted by the strike there.
No injuries were reported in Israel from the Qassam rockets. An earlier rocket, fired late Monday, damaged greenhouses.
Sources in Gaza suggested the three dead men were preparing to fire another rocket when their house was hit, Ynetnews said. People reported hearing explosions after the air strike and hospital employees said the bodies were scorched.
The air strikes occurred the day after a confrontation between Israeli commandos and a flotilla organized by peace activists. Nine people in the convoy were killed.