In 2001, while on his way to do camera work for the network in Afghanistan, he was arrested by the Pakistani army[2] and held in the United States Guantanamo Bay detainment camp in Cuba for over six years.

Stafford Smith also said that Al Hajj had witnessed "the Quran being flushed down the toilet by US soldiers in Afghanistan" and "expletives being written on the Muslim holy book".

[17] On 20 April 2007, the UK newspaper, The Guardian, started publishing excerpts from Clive Stafford Smith's book, Bad Men: Guantanamo Bay and the Secret Prisons.

He had to ask them to interrogate him about what he was supposed to have done wrong.In 1998, Al Hajj was treated for throat cancer and prescribed a course of anti-cancer drugs that he was to take every day for the rest of his life.

[20] On 22 August 2007, Clive Stafford Smith told Reporters Without Borders that he had found Al Hajj's health had seriously deteriorated since his last visit.

On 10 September 2007, Clive Stafford said that Al Hajj was focused on the worry that he would be the next captive to die and losing his ability to speak English.

[25][26] The file, dated 4 April 2008, describes Al Hajj as a high risk detainee with "direct ties to Al-Qaida, al-Haramayn non-governmental organization (NGO) and Taleban leadership."

According to the file, Al Hajj "admitted shipping supplies and carrying funds to Chechnya" but had "not been forthcoming regarding his activities in support of terrorist organizations as reported by other sources."

"[25] Among the reasons for Al Hajj's transfer to the facility, the file listed: To provide information on ... the al-Jazeera News Network's training program, telecommunications equipment, and newsgathering operations in Chechnya, Kosovo, and Afghanistan, including the network's acquisition of a video of UBL [Usama Bin Laden] and a subsequent interview with UBL.

"[29] The director of the Joint Intelligence Group, Paul Rester, said: "I consider the information that we obtained from him to be useful", though he declined to offer any substantiation for this claim.

Consistent with the law of armed conflict, the United States is entitled to hold enemy combatants until the end of hostilities, to prevent them from returning to the battlefield.

We will not put detainees or our operations at risk by discussing the possibility of transfers or releases before they take place.On the same day, Ali Sadiq, an official of the Sudanese Foreign Ministry, stated:[31] Last month, we received a memorandum from the US administration to the effect that they are considering Al Hajj's case and will hand down a final decision this month ... Based on this memo, we confirmed to the US administration in writing that Sami al-Hajj is an average Sudanese citizen with no extreme religious affiliations, he practices the religion like all other Sudanese citizens, and that in case he is released he will under no circumstances pose any threat to US security.

Al Jazeera showed footage of him being carried into the hospital on a stretcher, looking frail but smiling and surrounded by well-wishers.

[34] On January 29, 2021, the New York Review of Books published an open letter from al-Hajj, and six other individuals who were formerly held in Guantanamo, to newly inaugurated President Biden, appealing to him to close the detention camp.