Aware that the FBI wanted her for questioning, she left her parents' house 30 March 2003 with her three children.
According to her parents, she was going to go to Islamabad to visit her uncle but never arrived.
Around 25 March, the FBI put out a "worldwide alert" for Aafia and her ex-husband.

Siddiqui's and her children's whereabouts and activities from March 2003 to July 2008 are a matter of dispute.
Her supporters and the Pakistani government claim she was held as a prisoner by the US; the US government and others (including Suddiqui in her statements to the FBI immediately after her arrest) suggest she went into hiding with KSM's al-Baluchi family.

Starting 29 March, a "confusing series" of reports and denials of her arrest and detention appeared in Pakistan and the US.
On 1 April 2003, local newspapers reported and Pakistan interior ministry confirmed that a woman had been taken into custody on terrorism charges.
The Boston Globe described "sketchy" Pakistani news reports saying she had been detained for questioning by Pakistani authorities and the FBI.
However, a couple of days later, both the Pakistan government and the FBI publicly stated they were uninvolved in her disappearance.
Her sister Fauzia claimed Interior Minister Syed Faisal Saleh Hayat said that her sister had been released and would be returning home "shortly".

In 2003–04, the FBI and the Pakistani government said Siddiqui was still at large.
On 26 May 2004, US Attorney General John Ashcroft held a press conference described her as among the seven "most wanted" al-Qaeda fugitives and a "clear and present danger to the US".
Newsweek reported that she might be "the most immediately threatening suspect in the group".

One day before the announcement, however, The New York Times cited the US Department of Homeland Security saying there were no current risks; American Democrats accused the Bush administration of attempting to divert attention from plummeting poll numbers and to push the failings of the Invasion of Iraq off the front pages.

After her 2008 reappearance and arrest, Siddiqui told the FBI that she had at first gone into hiding with KSM's al-Baluchi clan (her lawyer later repudiated that statement) and worked at the Karachi Institute of Technology in 2005, was in Afghanistan in 2007, and also spent time in Quetta, Pakistan, sheltered by various people.
She told the FBI she met with Mufti Abu Lubaba Shah Mansoor, and according to the FBI had begun collecting materials on viruses for biological warfare.
According to an intelligence official in the Afghan Ministry of the Interior, her son, Ahmed, who was with her when she was arrested, said he and Siddiqui had worked in an office in Pakistan collecting money for poor people.
He told Afghan investigators that on 14 August 2008 they had traveled by road from Quetta to Afghanistan.
An Afghan intelligence official said he believes that Siddiqui was working with Jaish-e-Mohammed (the "Army of Muhammad"), a Pakistani Islamic mujahideen military group that fights in Kashmir and Afghanistan.

According to her ex-husband Khan, after the global alert for her was issued, Siddiqui went into hiding and worked for al-Qaeda.
During her disappearance, Khan said he saw her at Islamabad airport in April 2003 as she disembarked from a flight with their son; he said he helped Inter-Services Intelligence identify her.
He said he again saw her two years later, in a Karachi traffic jam.
Khan unsuccessfully sought custody of his son Ahmed and said most of the claims of Siddiqui's family in the Pakistani media relating to her and their children were one-sided and largely false.

In a signed affidavit, Siddiqui's maternal uncle, Shams ul-Hassan Faruqi, stated that on 22 January 2008 she visited him in Islamabad and told him she had been held by Pakistani agencies.
Knowing he had worked in Afghanistan and made contact with the Taliban in 1999, she asked for his help to cross into Taliban-controlled Afghanistan where she thought she would be safe.
He told her he was no longer in touch with them.
He notified his sister, Siddiqui'
Aware that the FBI wanted her for questioning, she left her parents' house 30 March 2003 with her three children. According to her parents, she was going to go to Islamabad to visit her uncle but never arrived. Around 25 March, the FBI put out a "worldwide alert" for Aafia and her ex-husband.
Siddiqui's and her children's whereabouts and activities from March 2003 to July 2008 are a matter of dispute. Her supporters and the Pakistani government claim she was held as a prisoner by the US; the US government and others (including Suddiqui in her statements to the FBI immediately after her arrest) suggest she went into hiding with KSM's al-Baluchi family.
Starting 29 March, a "confusing series" of reports and denials of her arrest and detention appeared in Pakistan and the US. On 1 April 2003, local newspapers reported and Pakistan interior ministry confirmed that a woman had been taken into custody on terrorism charges. The Boston Globe described "sketchy" Pakistani news reports saying she had been detained for questioning by Pakistani authorities and the FBI. However, a couple of days later, both the Pakistan government and the FBI publicly stated they were uninvolved in her disappearance. Her sister Fauzia claimed Interior Minister Syed Faisal Saleh Hayat said that her sister had been released and would be returning home "shortly".
In 2003–04, the FBI and the Pakistani government said Siddiqui was still at large. On 26 May 2004, US Attorney General John Ashcroft held a press conference described her as among the seven "most wanted" al-Qaeda fugitives and a "clear and present danger to the US". Newsweek reported that she might be "the most immediately threatening suspect in the group".
One day before the announcement, however, The New York Times cited the US Department of Homeland Security saying there were no current risks; American Democrats accused the Bush administration of attempting to divert attention from plummeting poll numbers and to push the failings of the Invasion of Iraq off the front pages.
After her 2008 reappearance and arrest, Siddiqui told the FBI that she had at first gone into hiding with KSM's al-Baluchi clan (her lawyer later repudiated that statement) and worked at the Karachi Institute of Technology in 2005, was in Afghanistan in 2007, and also spent time in Quetta, Pakistan, sheltered by various people. She told the FBI she met with Mufti Abu Lubaba Shah Mansoor, and according to the FBI had begun collecting materials on viruses for biological warfare. According to an intelligence official in the Afghan Ministry of the Interior, her son, Ahmed, who was with her when she was arrested, said he and Siddiqui had worked in an office in Pakistan collecting money for poor people. He told Afghan investigators that on 14 August 2008 they had traveled by road from Quetta to Afghanistan. An Afghan intelligence official said he believes that Siddiqui was working with Jaish-e-Mohammed (the "Army of Muhammad"), a Pakistani Islamic mujahideen military group that fights in Kashmir and Afghanistan.
According to her ex-husband Khan, after the global alert for her was issued, Siddiqui went into hiding and worked for al-Qaeda. During her disappearance, Khan said he saw her at Islamabad airport in April 2003 as she disembarked from a flight with their son; he said he helped Inter-Services Intelligence identify her. He said he again saw her two years later, in a Karachi traffic jam. Khan unsuccessfully sought custody of his son Ahmed and said most of the claims of Siddiqui's family in the Pakistani media relating to her and their children were one-sided and largely false.
In a signed affidavit, Siddiqui's maternal uncle, Shams ul-Hassan Faruqi, stated that on 22 January 2008 she visited him in Islamabad and told him she had been held by Pakistani agencies. Knowing he had worked in Afghanistan and made contact with the Taliban in 1999, she asked for his help to cross into Taliban-controlled Afghanistan where she thought she would be safe. He told her he was no longer in touch with them. He notified his sister, Siddiqui'
Aafia Siddiqui