They face charges of either "unlawful free speech" or "causing a harangue" or both, and could face a maximum of 60 day in jail.
Prosecutors had offered to drop the charges, but the protesters said they used the detainees' names in a symbolic move.
"When we were arraigned [it] was the first time their names had ever been spoken in a US court, today will be the second," Chris Brant, one of the protesters, told Al Jazeera.
A protester said in a statement ahead of the court proceedings that he would take the name of Yasser al-Zahrani, a Saudi Arabian prisoner who committed suicide in the camp in 2006.
"We will not exercise our rights when our country continues to deny the rights of others," Matthew Daloisio said in a statement quoted by AFP.
Another protester took the name of Sami al-Hajj, the Al Jazeera cameraman released from Guantanamo Bay earlier this month after six and a half years in the facility.
At least one of those on trial is a Catholic priest. The court proceedings could last until the end of the week.
Calls for closure
At present about 270 prisoners remain in the US facility in Guantanamo Bay, which remains one of the most controversial subjects of the so-called US war on terror.
There have been increasing calls for the facility to be closed and some senior US officials have acknowledged that the facility has damaged the US's image abroad.
Last week Robert Gates, the US defence secretary, said the US was "stuck" with the prison and said there are problems in repatriating some of those detained.
A series of military tribunals is planned for about 80 of the detainees, including the alleged planners of the September 11, 2001, attacks.