He was the first British officer to face criminal charges for challenging the legality of the war against Iraq. On 5 October 2005 he was charged with five counts of disobeying a lawful command between 1 June and 12 July 2005. Four of these relate to him refusing to carry out preparatory training with the final charge relating to his refusal to deploy to Iraq.
In a statement to the court martial at a pre-trial hearing in Aldershot, on 15 March 2006, Kendall-Smith said: "I am a leader. I am not a mere follower to whom no moral responsibility can be attached."
Philip Sapsford, QC, defending, told the court martial: "The flight lieutenant is entitled to advance before this tribunal that the use of force in Iraq was unlawful in international law," essentially reasoning that Kendall-Smith should be allowed to argue that any participation in the war effort was therefore unlawful. Sapsford added that the defence team was prepared to produce expert evidence to show that UN Resolution 1546, relied upon by the UK and US governments to justify the 2003 Invasion of Iraq, was no defence in international law. Sapsford also said he was considering calling former SAS soldier Ben Griffin, who recently resigned because of his objections to the war, to give evidence.
Prosecutors argued that the legal questions surrounding the invasion of Iraq were irrelevant and that the case should centre only around the official orders given to Kendall-Smith. Prosecutor David Perry argued that at the time Kendall-Smith refused to deploy, the invasion itself was over and British forces were in Iraq with the authority of U.N. Security Council resolutions passed after Saddam's fall.
A ruling on 22 March 2006, by the judge advocate Jack Bayliss, concurred. Bayliss dismissed Kendall-Smith's argument, ruling that he must face trial by court martial and would not be allowed to argue that the order to deploy was illegal. Obviating Kendall-Smith's argument that any participation in the war effort was unlawful on the basis of an illegal invasion, Bayliss asserted that British forces had full justification under UN resolutions 1511 and 1546 to be in Iraq at the time the charges were filed against Kendall-Smith in June and July, 2005. The judge advocate also rejected Kendall-Smith's claim that by serving in Iraq he could be complicit in a crime of aggression. Such a crime "cannot be committed by those in relatively junior positions such as that of the defendant. If a defendant believed that to go to Basra would make him complicit in the crime of aggression, his understanding of the law was wrong," Bayliss said.
A Court-martial in Aldershot sat from 11 to 13 April 2006. Kendall-Smith was found guilty on all five charges of disobeying orders, and sentenced to a penalty of eight months in prison  and ordered to pay £20,000 costs.
- Leppard, David (16 October 2005). "RAF officer faces jail over 'illegal war'". The Sunday Times (UK), 16 October 2005. London. Retrieved 17 October 2005.
- Payne, Stewart (16 March 2006). "RAF officer faces trial over 'illegal war' claim". The Daily Telegraph, 16 March 2006. London. Retrieved 19 March 2006.
- Halfpenny, Martin (15 March 2006). "RAF doctor faces court martial over stand on Iraq". The Independent, 15 March 2006. London. Archived from the original on 14 May 2006. Retrieved 19 March 2006.
- "RAF doctor jailed over Iraq refusal". London: The Guardian UK. 13 April 2006. Retrieved 5 May 2010.
- "Jail for Iraq refusal RAF doctor". BBC. 13 April 2006. Retrieved 5 May 2010.
- "RAF doctor must face Iraq court martial". Daily Mail Online. 22 March 2006. Retrieved 5 May 2010.