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The research for this story was supported by the Fund for Investigative Journalism. This article also appears online at TomDispatch.com. You can listen to an interview with Anand Gopal here. Ad Policy

One quiet, wintry night last year in the eastern Afghan town of Khost, a young government employee named Ismatullah simply vanished. He had last been seen in the town’s bazaar with a group of friends. Family members scoured Khost’s dusty streets for days. Village elders contacted Taliban commanders in the area who were wont to kidnap government workers, but they had never heard of the young man. Even the governor got involved, ordering his police to round up nettlesome criminal gangs that sometimes preyed on young bazaargoers for ransom.

But the hunt turned up nothing. Spring and summer came and went with no sign of Ismatullah. Then one day, long after the police and village elders had abandoned their search, a courier delivered a neat handwritten note on Red Cross stationery to the family. In it, Ismatullah informed them that he was in Bagram, an American prison more than 200 miles away. US forces had picked him up while he was on his way home from the bazaar, the terse letter stated, and he didn’t know when he would be freed.

In the past few years Pashtun villagers in Afghanistan’s rugged heartland have begun to lose faith in the American project. Many of them can point to the precise moment of this transformation, and it usually took place in the dead of night, when most of the country was fast asleep. In its attempt to stamp out the growing Taliban insurgency and Al Qaeda, the US military has been arresting suspects and sending them to one of a number of secret detention areas on military bases, often on the slightest suspicion and without the knowledge of their families. These night raids have become even more feared and hated in Afghanistan than coalition airstrikes. The raids and detentions, little known or understood outside the Pashtun villages, have been turning Afghans against the very forces many of them greeted as liberators just a few years ago.

One Dark Night in November

November 19, 2009, 3:15 am. A loud blast woke the villagers of a leafy neighborhood outside Ghazni, a city of ancient provenance in the country’s south. A team of US soldiers burst through the front gate of the home of Majidullah Qarar, the spokesman for Afghanistan’s agriculture minister. Qarar was in Kabul at the time, but his relatives were home, four of them sleeping in the family’s one-room guesthouse. One of them, Hamidullah, who sold carrots at the local bazaar, ran toward the door of the guesthouse. He was immediately shot but managed to crawl back inside, leaving a trail of blood behind him. Then Azim, a baker, darted toward his injured cousin. He, too, was shot and crumpled to the floor. The fallen men cried out to the two relatives–both of them children–remaining in the room. But they refused to move, glued to their beds in silent horror.

The foreign soldiers, most of them tattooed and bearded, then went on to the main compound. They threw clothes on the floor, smashed dinner plates and forced open closets. Finally they found the man they were looking for: Habib-ur-Rahman, a computer programmer and government employee. Rahman was responsible for converting Microsoft Windows from English to the local Pashto language so that government offices could use the software. The Afghan translator accompanying the soldiers said they were acting on a tip that Rahman was a member of Al Qaeda.

They took the barefoot Rahman and a cousin to a helicopter some distance away and transported them to a small American base in a neighboring province for interrogation. After two days, US forces released Rahman’s cousin. But Rahman has not been seen or heard from since.

“We’ve called his phone, but it doesn’t answer,” said his cousin Qarar, the agriculture minister’s spokesman. Using his powerful connections, Qarar enlisted local police, parliamentarians, the governor and even the agriculture minister himself in the search for his cousin, but they turned up nothing. Government officials who independently investigated the scene in the aftermath of the raid and corroborated the claims of the family also pressed for an answer as to why two of Qarar’s family members were killed. American forces issued a statement saying that the dead were “enemy militants [who] demonstrated hostile intent.”

Weeks after the raid, the family remains bitter. “Everyone in the area knew we were a family that worked for the government,” Qarar said. “Rahman couldn’t even leave the city, because if the Taliban caught him in the countryside they would have killed him.”

Beyond the question of Rahman’s guilt or innocence, it’s how he was taken that has left such a residue of hatred among his family. “Did they have to kill my cousins? Did they have to destroy our house?” Qarar asked. “They knew where Rahman worked. Couldn’t they have at least tried to come with a warrant in the daytime? We would have forced Rahman to comply.”

“I used to go on TV and argue that people should support this government and the foreigners,” he added. “But I was wrong. Why should anyone do so? I don’t care if I get fired for saying it, but that’s the truth.”

The Dogs of War

Night raids are only the first step in the American detention process in Afghanistan. Suspects are usually sent to one of a series of prisons on US military bases around the country. There are officially nine such jails, called Field Detention Sites in military parlance. They are small holding areas, often just a clutch of cells divided by plywood, and are mainly used for prisoner interrogations.

In the early years of the war, these were but way stations for those en route to Bagram prison, a facility with a notorious reputation for abusive behavior. As a spotlight of international attention fell on Bagram in recent years, wardens there cleaned up their act, and the mistreatment of prisoners began to shift to the little-noticed Field Detention Sites.

Of the twenty-four former detainees interviewed for this article, seventeen claim to have been abused at or en route to these sites. Doctors, government officials and the Afghan Independent Human Rights Commission, an independent Afghan body mandated by the Afghan Constitution to investigate abuse allegations, corroborate twelve of these claims.

One of these former detainees is Noor Agha Sher Khan, who used to be a police officer in Gardez, a mud-caked town in the eastern part of the country. According to Sher Khan, American forces detained him in a night raid in 2003 and brought him to a Field Detention Site at a nearby US base. “They interrogated me the whole night,” he recalled, “but I had nothing to tell them.” Sher Khan worked for a police commander whom US forces had detained on suspicion of having ties to the insurgency. He had occasionally acted as a driver for this commander, which made him suspicious in American eyes.

The interrogators blindfolded him, taped his mouth shut and chained him to the ceiling, he alleges. Occasionally they unleashed a dog, which repeatedly bit him. At one point they removed the blindfold and forced him to kneel on a long wooden bar. “They tied my hands to a pulley [above] and pushed me back and forth as the bar rolled across my shins. I screamed and screamed.” They then pushed him to the ground and forced him to swallow twelve bottles of water. “Two people held my mouth open, and they poured water down my throat until my stomach was full and I became unconscious,” he said. “It was as if someone had inflated me.” After he was roused, he vomited uncontrollably.

This continued for a number of days. Sometimes he was hung upside down from the ceiling, other times he was blindfolded for extended periods. Eventually he was moved to Bagram, where the torture ceased. Four months later he was quietly released, with a letter of apology from US authorities for wrongfully imprisoning him.

An investigation of Sher Khan’s case by the Afghan Independent Human Rights Commission and an independent doctor found that he had wounds consistent with the abusive treatment he alleges. American forces have declined to comment on the specifics of his case, but a spokesman said that some soldiers involved in detentions in this part of the country had been given unspecified “administrative punishments.” He added that “all detainees are treated humanely,” except for isolated cases.

The Disappeared

Some of those taken to the Field Detention Sites are deemed innocuous and never sent to Bagram. Even then, some allege abuse. Such was the case with Hajji Ehsanullah, snatched one winter night in 2008 from his home in the southern province of Zabul. He was taken to a detention site in Khost Province, some 200 miles away. He returned home thirteen days later, his skin scarred by dog bites and with memory difficulties that, according to his doctor, resulted from a blow to the head. American forces had dropped him off at a gas station in Khost after three days of interrogation. It took him ten more days to find his way home.

Others taken to these sites seem to have disappeared entirely. In the hardscrabble villages of the Pashtun south, where rumors grow more abundantly than the most bountiful crop, locals whisper tales of people who were captured and executed. Most have no evidence. But occasionally a body turns up. Such was the case at a detention site on a US military base in Helmand Province, where in 2003 a US military coroner wrote in the autopsy report of a detainee who died in US custody (later made available through the Freedom of Information Act): “Death caused by the multiple blunt force injuries to the lower torso and legs complicated by rhabdomyolysis (release of toxic byproducts into the system due to destruction of muscle). Manner of death is homicide.”

In the dust-swept province of Khost one day this past December, US forces launched a night raid on the village of Motai, killing six people and capturing nine, according to nearly a dozen local government authorities and witnesses. Two days later, the bodies of two of those detained–plastic cuffs binding their hands–were found more than a mile from the largest US base in the area. A US military spokesman denies any involvement in the deaths and declines to comment on the details of the raid. Local Afghan officials and tribal elders steadfastly maintain that the two were killed while in US custody. American authorities released four other villagers in subsequent days. The fate of the three remaining captives is unknown.

The matter could be cleared up if the US military were less secretive about its detention process. But secrecy has been the order of the day. The nine Field Detention Sites are enveloped in a blanket of official secrecy, but at least the Red Cross and other humanitarian organizations are aware of them. There may, however, be other sites whose existence on the scores of US and Afghan military bases that dot the country have not been disclosed. One example, according to former detainees, is a detention facility at Rish-Khor, an Afghan army base that sits atop a mountain overlooking the capital, Kabul.

One night last year US forces raided Zaiwalat, a tiny village that fits snugly into the mountains of Wardak Province, a few dozen miles west of Kabul, and netted nine locals. They brought the captives to Rish-Khor and interrogated them for three days. “They kept us in a container,” recalled Rehmatullah Muhammad, one of the nine. “It was made of steel. We were handcuffed for three days continuously. We barely slept those days.” The plain-clothed interrogators accused Muhammad and the others of giving food and shelter to the Taliban. The suspects were then sent to Bagram and released after four months. (A number of former detainees said they were interrogated by plainclothed officials, but they did not know if these officials belonged to the military, the CIA or private contractors.)

Afghan human rights campaigners worry that US forces may be using secret detention sites like the one allegedly at Rish-Khor to carry out interrogations away from prying eyes. The US military, however, denies even having knowledge of the facility.

The Black Jail

Much less secret is the final stop for most captives: the Bagram Theater Internment Facility. These days ominously dubbed “Obama’s Guantánamo,” Bagram nonetheless now offers the best conditions for captives during the entire detention process.

Its modern life as a prison began in 2002, when small numbers of detainees from throughout Asia were incarcerated there on the first leg of an odyssey that would eventually bring them to the US detention facility in Guantánamo, Cuba. In later years, however, it became the main destination for those caught within Afghanistan as part of the growing war there. By 2009 the inmate population had swelled to more than 700. Housed in a windowless old Soviet hangar, the prison consists of two rows of serried, cagelike cells bathed continuously in light. Guards walk along a platform that runs across the mesh tops of the pens, an easy position from which to supervise the prisoners below.

Regular, even infamous, abuse in the style of Iraq’s Abu Ghraib prison marked Bagram’s early years. Abdullah Mujahid, for example, was apprehended in the village of Kar Marchi in the eastern province of Paktia in 2003. Although Mujahid was a Tajik militia commander who had led an armed uprising against the Taliban in their waning days, US forces accused him of having ties to the insurgency. “In Bagram we were handcuffed, blindfolded and had our feet chained for days,” he recalled. “They didn’t allow us to sleep at all for thirteen days and nights.” A guard would strike his legs every time he dozed off. Daily, he could hear the screams of tortured inmates and the unmistakable sound of shackles dragging across the floor.

Then one day a team of soldiers dragged him to an aircraft but refused to tell him where he was going. Eventually he landed at another prison, where the air felt thick and wet. As he walked through the row of cages, inmates began to shout, “This is Guantánamo! You are in Guantánamo!” He would learn there that he was accused of leading the Pakistani Islamist group Lashkar-e-Taiba (which in reality was led by another person who had the same name and who died in 2006). The United States eventually released him and returned him to Afghanistan.

Former Bagram detainees allege that they were regularly beaten, subjected to blaring music twenty-four hours a day, prevented from sleeping, stripped naked and forced to assume what interrogators term “stress positions.” The nadir came in late 2002, when interrogators beat two inmates to death.

According to former detainees and organizations that work with them, the US Special Forces also run a second, secret prison somewhere on Bagram Air Base that the Red Cross still does not have access to. Used primarily for interrogations, it is so feared by prisoners that they have dubbed it the “Black Jail.”

One day two years ago, US forces came to get Noor Muhammad outside the town of Kajaki in the southern province of Helmand. Muhammad, a physician, was running a clinic that served all comers, including the Taliban. The soldiers raided his clinic and his home, killing five people (including two patients) and detaining both his father and him. The next day villagers found the handcuffed body of Muhammad’s father, apparently killed by a gunshot.

The soldiers took Muhammad to the Black Jail. “It was a tiny, narrow corridor, with lots of cells on both sides and a big steel gate and bright lights,” he said. “We didn’t know when it was night and when it was day.” He was held in a windowless concrete room in solitary confinement. Soldiers regularly dragged him by his neck and refused him food and water. They accused him of providing medical care to the insurgents, to which he replied, “I am a doctor. It’s my duty to provide care to every human being who comes to my clinic, whether they are Taliban or from the government.”

Eventually Muhammad was released, but he has since closed his clinic and left his home village. “I am scared of the Americans and the Taliban,” he said. “I’m happy my father is dead, so he doesn’t have to experience this hell.”

Afraid of the Dark

In the past two years American officials have moved to reform the main prison at Bagram, if not the Black Jail. Torture has stopped, and prison officials now boast that the typical inmate gains fifteen pounds while in custody. In the early months of this year, officials plan to open a dazzling new prison that will eventually replace Bagram, one with huge, airy cells, the latest medical equipment and rooms for vocational training. The Bagram prison itself will be handed over to the Afghans in the coming year, although the rest of the detention process will remain in US hands.

But human rights advocates say that concerns about the detention process remain. The US Supreme Court ruled in 2008 that inmates at Guantánamo cannot be stripped of their right to habeus corpus, but it stopped short of making the same argument for Bagram (officials say that since it is in the midst of a war zone, US civil rights legislation does not apply). Inmates there do not have access to a lawyer, as they do in Guantánamo. Most say they have no idea why they have been detained. They do now appear before a review panel every six months, which is intended to reassess their detention, but their ability to ask questions about their situation is limited. “I was only allowed to answer yes or no and not explain anything at my hearing,” said former detainee Rehmatullah Muhammad.

Nonetheless, the improvement in Bagram’s conditions begs the question: can the United States fight a cleaner war? That’s what Afghan war commander Gen. Stanley McChrystal promised last summer: fewer civilian casualties, fewer of the feared house raids and a more transparent detention process.

The American troops that operate under NATO command have begun to enforce stricter rules of engagement: they may now officially hold detainees for only ninety-six hours before transferring them to the Afghan authorities or freeing them, and Afghan forces must take the lead in house searches. American soldiers, when questioned, bristle at these restrictions–and have ways of circumventing them. “Sometimes we detain people, then, when the ninety-six hours are up, we transfer them to the Afghans,” said one marine who spoke on the condition of anonymity. “They rough them up a bit for us and then send them back to us for another ninety-six hours. This keeps going until we get what we want.”

A simpler way of dancing around the rules is to call in the Special Operations Forces–the Navy SEALs, Green Berets and others–which are not under NATO command and thus not bound by the stricter rules of engagement. These elite troops are behind most of the night raids and detentions in the search for “high-value suspects.” Military officials say in interviews that the new restrictions have not affected the number of raids and detentions at all. The actual change, however, is more subtle: the detention process has shifted almost entirely to areas and actors that can best avoid public scrutiny–small field prisons and Special Operations Forces.

The shift signals a deeper reality of war, say American soldiers: you can’t fight guerrillas without invasive raids and detentions, any more than you can fight them without bullets. Seen through the eyes of a US soldier, Afghanistan is a scary place. The men are bearded and turbaned. They pray incessantly. In most of the country, women are barred from leaving the house. Many Afghans own an assault rifle. “You can’t trust anyone,” said Rodrigo Arias, a marine based in the northeastern province of Kunar. “I’ve nearly been killed in ambushes, but the villagers don’t tell us anything. But they usually know something.”

An officer who has worked in the Field Detention Sites says that it takes dozens of raids to turn up a useful suspect. “Sometimes you’ve got to bust down doors. Sometimes you’ve got to twist arms. You have to cast a wide net, but when you get the right person, it makes all the difference.”

For Arias, it’s a matter of survival. “I want to go home in one piece. If that means rounding people up, then round them up.” To question this, he said, is to question whether the war itself is worth fighting. “That’s not my job. The people in Washington can figure that out.”

If night raids and detentions are an unavoidable part of modern counterinsurgency warfare, then so is the resentment they breed. “We were all happy when the Americans first came. We thought they would bring peace and stability,” said Rehmatullah Muhammad. “But now most people in my village want them to leave.” A year after Muhammad was released, his nephew was detained. Two months later, some other residents of Zaiwalat were seized. It has become a predictable pattern in Muhammad’s village: Taliban forces ambush American convoys as they pass through it, and then retreat into the thick fruit orchards nearby. The Americans return at night to pick up suspects. In the past two years, sixteen people have been taken and ten killed in night raids in this single village of about 300, according to villagers. In the same period, they say, the insurgents killed one local and did not take anyone hostage.

The people of Zaiwalat now fear the night raids more than the Taliban. There are nights when Muhammad’s children hear the distant thrum of a helicopter and rush into his room. He consoles them but admits he needs solace himself. “I know I should be too old for it,” he said, “but this war has made me afraid of the dark.”