A police officer said a house in the town of Mohammed al-Sakran, about 40 kilometers (25 miles) northeast of Baghdad, collapsed Tuesday night, killing the three children and their aunt. The parents were injured, he said.
He said five other people were injured when two mud houses collapsed in the outskirts of Baghdad's rundown Sadr City slum.
Two health officials confirmed the causality figures. All officials spoke on condition of anonymity as they were not authorized to release information to reporters.
Tuesday's rainstorm was heaviest in in the Baghdad this winter, flooding streets and forcing the government to declare an emergency public holiday.
Decades of war, international sanctions and underinvestment have battered Iraq's infrastructure. Billions of dollars have been spent since the 2003 U.S.-led invasion that toppled Saddam Hussein, but many projects have failed because of corruption.
Baghdad residents blamed their government for the damage.
"The heavy rain and lack of services the municipality of Baghdad should provide to citizens led to this catastrophe," said Abu Ibrahim, whose car was caught in a flooded underpass. "No good sewage, no drainage caused this bad situation."
In Sadr City, Alaa Ahmed's home was flooded, and his section of town was isolated from the outside world.
"Since yesterday, we have no electricity, we can't go out to buy food and I can't go to my work because all the roads are flooded," said Ahmed, a 34-year old father of two. "We are using bricks and wood panels to step on when we move between the rooms," he said.
Baghdad Governor Salah Abdul-Razzaq told the state-run TV that the authorities need three to four days to drain the streets, saying shelters were being set up for those who lost their houses.