Gaunt looking men are huddled together in stifling rooms where they are accused of waging jihad in the Middle East.
But many of those stuck in the makeshift cells say they are ordinary citizens.
As Iraqi forces push to liberate the last of western Mosul, jails are filling in the south.
In one prison, 1,150 detainees have passed through in a three months, while officer guarding the jail said conditions are dire.
He said: “Prisoners are infected with diseases, lots of health and skin problems, because they’re not exposed to the sun.
“The majority can’t walk. Their legs are swollen because they can’t move.”
In the Qayara air base, south of Mosul, 2,800 prisoners are being held.
Prisoners protested their innocence in secretive interviews with news agency AP.
One prisoner said: “You won’t find 10 real (ISIS members) among these guys. And all of them have spent more than six months here.
“Since I got here eight months ago, I’ve only seen the sun once.”
The prisoner said he was a civil servant and had travelled between Baghdad and Mosul many times before his arrest.
He said: “They said my name was in their database. I haven’t seen any court or judge. I don’t even know what I’m accused of. A lot of names are the same.”
Some prisoners claimed their conditions are so bad they are taken to hospital to have infection wounds treated an usually return with amputations.
Others have allegedly died in holding cells.
Another prisoner said: “We really want to die.
“None of us have received any visitors, relatives, family members. They don’t even know where we are.”
Human rights violations were acknowledged by prime minister Haider al-Abadi but he claimed they were acts of lone soldiers.
The fight against ISIS is personal for many of those in the Iraqi forces whose families were slaughtered by the terrorists.
Reports claim they have sought bloody vengeance and have tortured people for information on certain jihadis, and shot them dead.
One soldier is looking for the pair who killed his father.
The lieutenant keeps a picture of the two men on his phone.
He said: “Most of them I just asked questions but for those who I knew had blood on their hands, I killed them on the spot.”
“I’m not selfish with my revenge, what I’m doing is for all Iraqis.”
Horror videos have emerged of ISIS suspects being thrown from a high wall next to the Tigris River by Iraqi forces.
In June, Human Rights Watch said extrajudicial killings are taking place “basically everywhere that is touched by this conflict” and by every armed force involved in the fight.
Soldiers like the lieutenant claim there is no reliable justice system and an ISIS fighter could bribe their way to freedom.
The Iraqi Governmeant said military says troops have orders to hand any captured ISIS over for interrogation ahead of future trial.
The soldier said: “I know some people believe that this kind of killing is wrong, but Daesh, they are not human beings.
“I am the one who still has my humanity.
“I hope I find him alive.
“Because I want to make sure he dies a slow death, not quick. I want him to tell me where my father’s body is buried, and then I want to take his body and hang it from a post in my village.”