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In 2001, when covering events in Afghanistan with the Northern Alliance, he and French journalist Véronique Reyberotte survived an attack by the Taliban which killed journalists Volker Handloik, Johanne Sutton, and Pierre Billaud. He was awarded the 2003 Walkley Award for Journalism Leadership in recognition of acts of courage and bravery in the practice of journalism.
Detainment in Israel
In 2010, McGeough travelled on a Gaza-bound flotilla, reporting for The Sydney Morning Herald and Brisbane Times from aboard the MV Samoud (also known as the MV Challenger I). When Israeli forces boarded the flotilla's vessels on 31 May, McGeough and Herald photographer Kate Geraghty were among those detained. In an audio transmission sent shortly before the MV Samoud was intercepted, he said:
"At 4.20(am local time) (11.20am Sydney time) we realised all communications on the boat were jammed, 4.22 (am) – we see two zodiacs moving in, pressing through. Two more zodiacs. Now there are five of them astern of us. There's white wakes on black water. Search lights on one of the cargo ships and from the Turkish ferry are picking up the zodiacs now."
The following day, Fairfax confirmed that McGeough had, along with Geraghty, been detained by Israel in the city of Beersheba. According to the Herald's editor Peter Fray, McGeough turned down the option of being deported immediately, in return for signing a form in which he would have admitted entering Israel illegally. When meeting with Australian and Irish consular officials in Beersheba's Ela prison, McGeough told them that he intended to challenge attempts by Israeli authorities to deport him.
However, Australia's Department of Foreign Affairs and Trade and the Herald confirmed on 3 June that both McGeough and Geraghty had been taken to Ben Gurion International Airport in Tel Aviv to be deported. McGeough said that he had left "on legal advice that we will be able to appeal our deportation in absentia".
Speaking to the Herald from Istanbul, McGeough described his treatment as "an absolute disrespect by Israel", accusing Israeli authorities of "a total disrespect to the fundamentals of democracy, and the fundamentals of the rights of journalists under the Geneva Convention".
- 2003 Walkley Award for Journalism Leadership
- 2010 Douglas Stewart award and Book of the Year for "Kill Khalid" at the 2010 New South Wales Premier's Literary Awards 
- Infernal Triangle Conflict in Iraq, Afghanistan and The Levant - Eyewitness reports from the September 11 decade, Allen & Unwin, 2011, ISBN 978-1-74237-563-2
- Kill Khalid: Mossad's failed hit ... and the rise of Hamas, Allen & Unwin, 2009, ISBN 978-1-74175-600-5
- Manhattan to Baghdad : despatches from the frontline in the War on Terror, Allen & Unwin, 2003, ISBN 978-1-74114-025-5
- In Baghdad: a reporter's war, Allen & Unwin, 2003, ISBN 978-1-74114-219-8
- Mission impossible: the sheiks, the U.S. and the future of Iraq, Black Inc., 2004, ISBN 978-1-86395-165-4
- Kill Khalid (Foreign Affairs): "gem of leave-no-stone-unturned reporting".
- Kill Khalid (Washington Post): "... timely and thorough examination of Hamas, highlighting the ways in which Israel has intentionally and unintentionally aided its rise."
- "Notes from the Freedom Flotilla before it was attacked by Israeli forces | Palestine". Axisoflogic.com. Retrieved 26 October 2010.
- "Protesters bound for Gaza". Brisbanetimes.com.au. Retrieved 26 October 2010.
- A NATION CHALLENGED: THE NEWS MEDIA; Two French Radio Journalists and a German Are Killed in Taliban Ambush of a Rebel Force, The New York Times, 13 November 2001
- "Aboard MV Blue Marmara". Brisbanetimes.com.au. 31 May 2010. Retrieved 26 October 2010.
- "Paul McGeough, Kate Geraghty on convoy boat during Israeli attack". AAP. 31 May 2010. Retrieved 4 June 2010.
- "Fairfax journalists safe, but in jail". The Spy Report (Media Spy). 1 June 2010. Retrieved 4 June 2010.
- "McGeough plans to fight Israeli deportation". The Spy Report (Media Spy). 2 June 2010. Retrieved 4 June 2010.
- "Fairfax journalists among deportees from Israel". The Spy Report (Media Spy). 3 June 2010. Retrieved 4 June 2010.
- "McGeough: "Deportation is an absolute disrespect"". The Spy Report (Media Spy). 3 June 2010. Retrieved 4 June 2010.
- Jamal, Nadia (3 June 2010). "Freed journos tell of Israeli commandos like 'hyenas hunting'". The Sydney Morning Herald. Retrieved 4 June 2010.
- http://www.pla.nsw.gov.au/ NSW Premiers Literary Awards
- "Kill Khalid: The Failed Mossad Assassination of Khalid Mishal and the Rise of Hamas". Foreign Affairs. 1 September 2009. Retrieved 26 October 2010.
- "The Martyr Who Did Not Die", The Washington Post, GREG MYRE, 8 March 2009; Page B01
- "Q and A: Paul McGeough", Columbia Journalism Review, Katia Bachko, 11 February 2009
- "Paul McGeough reads from Kill Khalid", Vanity Fair, 24 March 2009
- "Paul McGeough’s ‘Kill Khalid’", WBUR: On Point 29 July 2009