Survivors tell of damaged lives after being deliberately infected in secret 1940s experiment on 1,500 men, women and children

Marta Orellana says she was playing with friends at the orphanage when the summons sounded: "Orellana to the infirmary. Orellana to the infirmary."

Waiting for her were several doctors she had never seen before. Tall men with fair complexions who spoke what she guessed was English, plus a Guatemalan doctor. They had syringes and little bottles.

They ordered her to lie down and open her legs. Embarrassed, she locked her knees together and shook her head. The Guatemalan medic slapped her cheek and she began to cry. "I did what I was told," she recalls.

Today the nine-year-old girl is a rheumy-eyed 74-year-old great-grandmother, but the anguish of that moment endures. It was how it all began: the pain, the humiliation, the mystery.

It was 1946 and orphans in Guatemala City, along with prisoners, military conscripts and prostitutes, had been selected for a medical experiment which would torment many, and remain secret, for more than six decades.

The US, worried about GIs returning home with sexual diseases, infected an estimated 1,500 Guatemalans with syphilis, gonorrhea and chancroid to test an early antibiotic, penicillin.

"They never told me what they were doing, never gave me a chance to say no," Orellana said this week, seated in her ramshackle Guatemala City home. "I've lived almost my whole life without knowing the truth. May God forgive them."

The US government admitted to the experiment in October when the secretary of state, Hillary Clinton, and the health secretary, Kathleen Sebelius, issued a joint statement apologising for "such reprehensible research" under the guise of public health. Barack Obama phoned his Guatemalan counterpart, Alvaro Colom, to say sorry too.

Susan Reverby, a professor at Wellesley College in the US, uncovered the experiment while researching the Tuskegee syphilis study in which hundreds of African American men were left untreated for 40 years from the 1930s.

The Guatemalan study went further by deliberately infecting its subjects. Not only did it violate the hippocratic oath to do no harm but it echoed Nazi crimes exposed around the same time at the Nuremberg trials.

The victims remained largely unknown but the Guardian has interviewed the families of the three survivors identified so far by Guatemala. They chronicled lives blighted by illness, neglect and unanswered questions.

"My father didn't know how to read and they treated him like an animal," said Benjamin Ramos, 57, the son of Federico, 87, a former soldier. "This was the devil's experiment."

Mateo Gudiel, 57, said his father, Manuel, 87, another ex-conscript, has syphilis-linked infections, dementia and headaches. "Some of this has been passed on to me, my siblings and our children." Children can inherit congenital syphilis.

More than half of the subjects were low-ranking soldiers delivered by their superiors to US physicians working from a military base in the capital. The Americans initially arranged for infected prostitutes to have sex with prisoners before discovering it was more "efficient" to inject soldiers, psychiatric patients and orphans with the bacterium.

Guatemala's official inquiry, headed by its vice-president, is due to publish its report in June. "What impacted me the most was how little value was given to these human lives. They were seen as things to be experimented on," said Carlos Mejia, a member of the inquiry and head of the Guatemalan College of Physicians.

The US scientists treated 87% of those infected with syphilis and lost track of the other 13%. Of those treated about a tenth suffered recurrences.

The US medical establishment, including the surgeon-general, keenly followed the study even though John Cutler, who led the Guatemala team, acknowledged ethical violations in a 1947 letter, saying: "Unless the law winks occasionally, you have no progress in medicine."

His supervisor, RC Arnold, urged discretion. "If some goody organisation got wind of the work there would be a lot of smoke." In the end the study yielded no useful information and was buried.

Guatemalan co-operation was won by offering cigarettes to subjects and material to resource-starved institutions. Psychiatric patients who could not give their own names were registered under nicknames such as the "mute of St Marcos".

It is unclear what, if anything, was promised to the Sisters of Charity in return for supplying orphans to the tall men in white coats who visited each week from 1946-48.

"They didn't tell me why they singled me out," said Orellana, who was four when sent to the institution after her parents died. After the initial gynaecological probing, when she assumes she was infected, she was given penicillin weekly. "My body hurt and I was sleepy, I didn't want to play." At least 10 other girls were also picked for the study, she added.

The treatment failed – but even as an adult, when she worked as a maid and in factories, doctors would say only that she had "bad blood", leaving her ailments a mystery. A "loving and patient" husband helped her overcome intimacy issues. She has five children, 20 grandchildren and eight great-grandchildren.

When the US finally owned up to the scandal in 2010 Orellana, near crippled from a stroke but still lucid, was mesmerised. She tested positive for syphilis, said Rudy Zuniga, a lawyer who is representing alleged victims in a class action in the US. Only a handful of the original 1,500 may still be alive but there could be dozens if not hundreds of infected children and grandchildren, he said.

Pablo Werner, a human rights lawyer who is investigating the case, doubted Guatemala would accept responsibility let alone pay compensation for its complicity in the experiment. "Our judicial system is not famous for speed or fairness. Even if the Guatemalan doctors who participated in this are dead their families still have connections," he said.

With the few survivors ailing, their Guatemalan and US lawyers hope to negotiate speedy compensation with US officials at a meeting due in August, said Zuniga. If that fails the case will go to a Washington district court and could last years.

For Orellana the resolution of her life's mystery, published in local media, has come with a catch. The criminal gangs which plague Guatemala City think she received a huge payout and are making threats, demanding a cut.