The government had handed over 39 cases to military authorities last week for trial, of which 12 were transferred to military courts.
This is the first batch of cases placed before the newly established courts for which the government has amended the constitution and the Army Act.
The 12 cases being tried include six from Khyber Pakhtunkhwa, five from Punjab and one from Sindh, a military spokesman said.
On Thursday, Inter-Services Public Relations chief Maj. Gen. Asim Bajwa said that one of the cases was related to killing of 13 Frontier Corps troopers and another involved the killing of NGO workers.
Other cases were related to handlers and facilitators of suicide attacks, Maj. Gen. Bajwa said.
All those being tried by military courts are hard core terrorists, he added.