Afrah al-Qaisi is an outspoken critic of government institutions in satirical columns she writes for several local newspapers and media outlets. Qaisi used to work for the pan-Arab, Saudi-owned newspaper Asharq al-Awsat.
Iraq's Interior Ministry said in a statement it had formed a team to look into her abduction.
The gunmen took Qaisi from the predominantly Sunni southern Saydiya district of the capital where she lived with her family, according to Ziyad al-Ajili, head of the Iraqi Journalistic Freedoms Observatory.
"They separated the children from their mother after forcefully entering the house and took money, jewellery, laptops and her car as they left," Ajili said.
Her husband was away at the time and the assailants broke into the house after Qaisi refused to open the door.
Iraq is ranked second after Somalia in the Committee to Protect Journalists (CPJ) 2016 Index of Impunity, which calculates the number of unsolved murders over a 10-year period as a percentage of each country's population.
Over the past decade, 71 journalists have been killed with impunity in Iraq, according to the CPJ.
Many were victims of Sunni insurgents who were active in Iraq even before Islamic State militants overran around one third of the country more than two years ago.
But other armed factions, including Shi'ite militias, some backed by the government, have grown increasingly powerful through their participation in Baghdad's fight against Islamic State.
Afrah al-Qaisi is an outspoken critic of government institutions in satirical columns she writes for several local newspapers and media outlets.
An Iraqi journalist was kidnapped by unidentified gunmen from her home in Baghdad overnight, police and relatives said on Tuesday, prompting Prime Minister Haider al-Abadi to order an investigation.
