Captain Derrick Grace, a lawyer representing the prosecution, said: "The accused was supposed to deploy with his unit to face hazardous duty in Iraq. His service was going to be important as a medic regardless of whether he was carrying a weapon or not."
"But instead the accused decided to jump out of his window and run away."
A deserter is defined by the US department of defence as a member of the armed forces who is absent from their unit or post without authorisation, quits their unit to avoid duty or enlists improperly in another service.
It can also apply to people who are absent without leave for 30 straight days or more.
The US defence department recorded a total of 4,494 deserters in 2005, according to official data.
In addition to Aguayo and Watada, there have been several similar cases, including that of Malcolm Kendall-Smith, a British air force doctor who was sentenced to eight months in jail last April for refusing to go to Iraq.
Amnesty International said it had sent a delegate to observe the court martial proceedings to assess whether Aguayo would be a prisoner of conscience if convicted and imprisoned.