Rory Carroll, 33, who is the Guardian's Baghdad correspondent, was on assignment when he vanished, the paper said in a statement on Wednesday.
"It is believed Mr Carroll may have been taken by a group of armed men," the statement said. "The Guardian is urgently seeking information about Mr Carroll's whereabouts and condition."
Carroll's father, Joe, said The Guardian told him three people had been with his son when he was abducted, "and one of them did get a bit roughed up but he was the only one kidnapped".
Carrol has been based in Baghdad for nine months and previously reported from South Africa and Rome.
The veteran journalist had broadcast a live report on the trial of Saddam Hussein on the Romanian news channel Realitatea TV earlier on Wednesday.
Saddam trial story
Realitatea TV said Carroll had been kidnapped after trying to learn what ordinary Iraqis thought of the trial. Joe Carroll, a former correspondent for the Irish Times newspaper, said his son had tried to reassure him about his safety in Baghdad.
"There are grounds for suspecting that tension linked to the start of Saddam Hussein's trial are having repercussions on the press"
Reporters Without Borders statement
Armed men in Iraq have kidnapped more than 220 foreigners and killed nearly 40.
The press freedom group Reporters Without Borders said 72 journalists and their assistants had died in Iraq since the start of the war in March 2003
"Past experience with journalists being taken hostage in Iraq showed that a significant expression of support in the first few hours after the kidnapping were vital," the group said in a statement.
"Unfortunately, the safety of journalists is still far from being assured in Iraq and there are grounds for suspecting that tension linked to the start of Saddam Hussein's trial are having repercussions on the press," it said.