Before the United States permitted a terrifying way of interrogating prisoners, government lawyers and intelligence officials assured themselves of one crucial outcome. They knew that the methods inflicted on terrorism suspects would be painful, shocking and far beyond what the country had ever accepted. But none of it, they concluded, would cause long-lasting psychological harm.

Fifteen years later, it is clear they were wrong.

Today in Slovakia, Hussein al-Marfadi describes permanent headaches and disturbed sleep, plagued by memories of dogs inside a blackened jail. In Kazakhstan, Lutfi bin Ali is haunted by nightmares of suffocating at the bottom of a well. In Libya, the radio from a passing car spurs rage in Majid Mokhtar Sasy al-Maghrebi, reminding him of the CIA prison where earsplitting music was just one assault to his senses.

And then there is the despair of men who say they are no longer themselves. “I am living this kind of depression,” said Younous Chekkouri, a Moroccan, who fears going outside because he sees faces in crowds as Guantánamo Bay guards. “I’m not normal anymore.”

After enduring agonizing treatment in secret CIA prisons around the world or coercive practices at the military detention camp at Guantánamo Bay, Cuba, dozens of detainees developed persistent mental health problems, according to previously undisclosed medical records, government documents and interviews with former prisoners and military and civilian doctors. Some emerged with the same symptoms as U.S. prisoners of war who were brutalized decades earlier by some of the world’s cruelest regimes.

Those subjected to the tactics included victims of mistaken identity or flimsy evidence that the United States later disavowed. Others were foot soldiers for the Taliban or al-Qaida who were later deemed to pose little threat. Some were hardened terrorists, including those accused of plotting the Sept. 11 attacks or the 2000 bombing of the U.S. destroyer Cole. In several cases, their mental status has complicated the nation’s long effort to bring them to justice.

Americans have long debated the legacy of post-Sept. 11 interrogation methods, asking whether they amounted to torture or succeeded in extracting intelligence. But even as President Barack Obama continues transferring people from Guantánamo and Donald Trump, the Republican presidential nominee, promises to bring back techniques, now banned, such as waterboarding, the human toll has gone largely uncalculated.

At least half of the 39 people who went through the CIA’s “enhanced interrogation” program, which included depriving them of sleep, dousing them with ice water, slamming them into walls and locking them in coffin-like boxes, have since shown psychiatric problems, The New York Times found. Some have been diagnosed with post-traumatic stress disorder, paranoia, depression or psychosis.

Hundreds more detainees moved through CIA “black sites” or Guantánamo, where the military inflicted sensory deprivation, isolation, menacing with dogs and other tactics on men who now show serious damage. Nearly all have been released.

“There is no question that these tactics were entirely inconsistent with our values as Americans, and their consequences present lasting challenges for us as a country and for the individuals involved,” said Ben Rhodes, the deputy national security adviser.

The U.S. government has never studied the long-term psychological effects of the extraordinary interrogation practices it embraced. A Defense Department spokeswoman, asked about long-term mental harm, responded that prisoners were treated humanely and had access to excellent care. A CIA spokesman declined to comment.

Researchers caution that it can be difficult to determine cause and effect with mental illness. Some prisoners of the CIA and the military had underlying psychological problems that may have made them more susceptible to long-term difficulties; others appeared to have been remarkably resilient. Incarceration, particularly the indefinite detention without charges that the United States devised, is inherently stressful. Still, outside medical consultants and former government officials said they saw a pattern connecting the harsh practices to psychiatric issues.

Those treating prisoners at Guantánamo for mental health issues typically did not ask their patients what had happened during their questioning. Some physicians, though, saw evidence of mental harm almost immediately.

After prisoners were released from U.S. custody, some found neither help nor relief. Mohammed Abdullah Saleh al-Asad, a businessman in Tanzania, and others were snatched, interrogated and imprisoned, then sent home without explanation. They returned to their families deeply scarred from interrogations, isolation and the shame of sexual taunts, forced nudity, aggressive body cavity searches and being kept in diapers.

Asad, who died in May, was held for more than a year in several secret CIA prisons. “Sometimes, between husband and wife, he would admit to how awful he felt,” his widow, Zahra Mohamed, wrote in a statement prepared for the African Commission on Human and Peoples’ Rights. “He was humiliated, and that feeling never went away.”

‘A Human Mop’

In a cold room once used for interrogations at Guantánamo, Stephen N. Xenakis, a former military psychiatrist, faced a onetime al-Qaida child soldier, Omar Khadr. It was December 2008, and this evaluation had been two years in the making.

Khadr, a Canadian citizen, had been wounded and captured in a firefight at age 15 at a suspected terrorist compound in Afghanistan, where, he said, he had been sent to translate for foreign fighters by his father, a member of al-Qaida. Years later, he would plead guilty to war crimes, including throwing a grenade that killed an Army medic. At the time, though, he was the youngest prisoner at Guantánamo.

He told his lawyers that the U.S. soldiers had kept him from sleeping, spit in his face and threatened him with rape. In one meeting with the psychiatrist, Khadr, then 22, began to sweat and fan himself, despite the air-conditioned chill. He tugged his shirt off, and Xenakis realized that he was witnessing an anxiety attack.

When it happened again, Khadr explained that he had once urinated during an interrogation and soldiers had dragged him through the mess. “This is the room where they used me as a human mop,” he said.

Xenakis found that Khadr had PTSD, a conclusion the military contested. Many of Xenakis’ diagnoses in other cases remain classified or sealed by court order, but he said he consistently found links between harsh U.S. interrogation methods and psychiatric disorders.

Back home in Virginia, Xenakis delved into research on the effects of abusive practices. He found decades of papers on the issue — science that had not been considered when the government began crafting new interrogation policies after Sept. 11.

At the end of the Vietnam War, military doctors noticed that former prisoners of war developed psychiatric disorders far more often than other soldiers, an observation also made of former POWs from World War II and the Korean War. The data could not be explained by imprisonment alone, researchers found. Former soldiers who suffered torture or mistreatment were more likely than others to develop long-term problems.

By the mid-1980s, the Veterans Administration had linked such treatment to memory loss, an exaggerated startle reflex, horrific nightmares, headaches and an inability to concentrate. Studies noted similar symptoms among torture survivors in South Africa, Turkey and Chile. Such research helped lay the groundwork for how American doctors now treat combat veterans.

“In hindsight, that should have come to the fore” in the post-Sept. 11 interrogation debate, said John Rizzo, the CIA’s top lawyer at the time. “I don’t think the long-term effects were ever explored in any real depth.”

Instead, the government relied on data from a training program to resist enemy interrogators, called SERE, for Survival, Evasion, Resistance and Escape. The military concluded there was little evidence that disrupted sleep, near-starvation, nudity and extreme temperatures harmed military trainees in controlled scenarios.

Two veteran SERE psychologists, James Mitchell and Bruce Jessen, worked with the CIA and the Pentagon to help develop interrogation tactics. They based their strategies in part on the theory of “learned helplessness,” a phrase coined by the U.S. psychologist Martin E.P. Seligman in the late 1960s. He gave electric shocks to dogs and discovered that they stopped resisting once they learned they could not stop the shocks. If the United States could make men helpless, the thinking went, they would give up their secrets.

In the end, Justice Department lawyers concluded that the methods did not constitute torture, which is illegal under U.S. and international law. In a series of memos, they wrote that no evidence existed that “significant psychological harm of significant duration, e.g., lasting for months or even years” would result.

With fear of another terrorist attack, there was little incentive or time to find contrary evidence, Rizzo said. “The government wanted a solution,” he recalled. “It wanted a path to get these guys to talk.”

At least 119 men moved through the CIA jails, where the interrogations were designed to disrupt the senses and increase helplessness — factors that researchers decades earlier had said could make people more susceptible to psychological harm. Forced nudity, sensory deprivation and endless light or dark were considered routine.

Today at Guantánamo Bay, the Caribbean landscape is reclaiming the relics of the U.S. detention system. Weeds overtake fences in abandoned areas of the prison complex. Guard towers sit empty. It is eerily quiet.

Obama banned coercive questioning on his second day in office, and his administration has whittled the prison population to 61, down from nearly 700 at its peak. Interrogations ended long ago. Except for the so-called high-value detainees, kept in a building hidden in the hills, most of the remaining prisoners share a concrete jail called Camp 6.

Asked about their psychological well-being, Rear Adm. Peter J. Clarke, the commander at Guantánamo, said in an interview: “What I observe are detainees who are well-adjusted, and I see no indications of ill effects of anything that may have happened in the past.”

It has been difficult to determine the scale of mental health problems at Guantánamo, much less how many cases are linked to the treatment the prisoners endured. Most medical records remain classified. Anecdotal accounts, though, have emerged over the years.

One of the few official glimpses into the population came in a 2006 medical journal article. Two military psychologists and a psychiatrist at Guantánamo wrote that about 11 percent of detainees were then receiving mental health services, a rate lower than that in civilian jails or among former U.S. prisoners of war. The authors acknowledged, however, that Guantánamo doctors faced significant challenges in diagnosing mental illness, most notably the difficulty in building trust. Many prisoners, including some with serious mental health conditions, refused evaluation and treatment, the study noted, which would have lowered the count.

Five years later, Xenakis and Vincent Iacopino, the medical director for Physicians for Human Rights, published research about nine prisoners who exhibited psychological symptoms after undergoing interrogation tactics — a hose forced into a mouth, a head held in a toilet, death threats — by U.S. jailers.

The two based their study on the medical records and interrogation files of the prisoners, all of whom had arrived at Guantánamo in its first year, had never been in CIA custody and were never charged with any crimes. In none of those cases, the study said, did Guantánamo doctors document any inquiries into whether the symptoms were tied to interrogation tactics.