American troops have been called in to help the investigation and Iraqi Prime Minister Nouri Maliki has pledged that the perpetrators will be brought to justice.
Mr Obama said in a statement: "I strongly condemn these outrageous attacks on the Iraqi people, and send my deepest condolences to those who have lost loved ones.
"These bombings serve no purpose other than the murder of innocent men, women and children, and they only reveal the hateful and destructive agenda of those who would deny the Iraqi people the future that they deserve."
As Mr Maliki visited the scene of the attacks on Sunday, he blamed al-Qaeda and supporters of former president Saddam Hussein.
"These cowardly terrorist attacks must not affect the determination of the Iraqi people to continue their struggle against the remnants of the dismantled regime and al-Qaeda terrorists," he said.
Overall, violence has dropped dramatically in Iraq compared to a year ago, although sporadic attacks still continue in several parts of the country.
But correspondents say there are fears that violence may increase as the country heads towards parliamentary elections scheduled for the beginning of next year.
The bombs went off as senior politicians were meeting in central Baghdad to try to break the deadlock over a draft law that would enable elections to take place in January.
The meeting ended without agreement, but will re-convene on Monday.
Last week the Iraqi parliament failed to meet a deadline to pass the legislation because of differences on a number of issues, among them whether to tell voters which candidates are on the party lists.
The US government, which has around 120,000 soldiers stationed in Iraq, says it wants all combat troops out by the end of August 2010 in preparation for a full military withdrawal by 2012.
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