Call her Hanan. She sits in front of me, a red scarf tied round her long intelligent face, her wide, bright eyes sparkling as she tells her story, her two-year-old son Omar restless on the chair beside her. To save the "honour" of her family – and to avoid being killed by her youngest brother – she has married her own rapist. To save the "honour" of her family – to stay alive – she is now divorcing her rapist. Omar, drinking orange juice, jumping on his plastic chair, is the rapist's son.

Hanan is the victim of a vast, corrupt system of "honour" crimes that plagues the Middle East, and takes the lives of at least 5,000 women – perhaps four times that number – a year, a vicious patriarchal system of extra-judicial killings in which a chance conversation between an unmarried woman and a stranger, a mere rumour of extra-marital relations – let alone sexual relations – leads to death by throat-cutting, strangulation, beheading or shooting. These executions – usually by members of the women's own family – are almost always committed in secret. They are always brutal. They are a scourge on society. Policemen and judges often connive with the murderers.

Hanan is a Palestinian Sunni Muslim, raped in her own home in Jordan by another Palestinian, but "honour" crimes are neither a uniquely Muslim phenomenon nor a religious tradition. Christians practice the "honour killing" of women. So do Hindus. From south-east Turkey and Iraqi Kurdistan to Pakistan and India, in Egypt and Gaza and the West Bank – across an area far wider than the old Ottoman empire – women are shamefully murdered to "cleanse" their families amid the squalor of mountain villages, refugee camps and city slums. "Honour" crimes are the greatest taboo of the region which, through emigration, has spread to Europe and the Americas.

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Hanan has been lucky – so far. She tells her story with courage, sitting beside the women who run a shelter in Amman for Jordan's potential "honour" victims. But 31-year-old Hanan is also frightened. Exactly a week after we met, a Jordanian man confessed to killing his 16-year-old niece to save his family's "honour" after she was sexually assaulted – Hanan's own tragedy – by a 17-year-old who took her virginity. The uncle fired 30 machine-gun rounds at his niece at Deir Alla, close to Amman, "to cleanse the family honour", although other members of his family had already married the girl off to a cousin in the hope of concealing the rape.

"My father is blind and I was living with him in a very small house, looking after him when he wasn't selling feather dusters," Hanan says. "The rest of my family – my mother, three brothers and two sisters – live elsewhere. All I did was look after my father. Then one afternoon when my father was at work, I went to take a nap. But I woke up to find a man on top of me. He was a thief who had got in through the roof and I couldn't get him off me. I could do nothing. I screamed and screamed but no one heard me and he raped me. He was a rough-looking man , with the scar of a knife wound on his cheek and tattoos on his arms. I think he was drunk because he smelled of alcohol. He was like a demon.

"I tried to commit suicide the same afternoon, so I wouldn't have to tell my father what had happened. I swallowed a whole pack of pills. Nothing happened – but I slept for two whole days. I wanted to tell my father, but I didn't tell him for another 10 days. When I did, he was very upset and he was crying. He got sick and at one point they were going to take him to hospital. Then he said to me: 'No one knows and no one needs to know, so we can keep it between us. But after a month and a half, I had symptoms like I was pregnant – still, I didn't tell my father this for another two months. I was too shy. But my period didn't come for three months. My father then told me to go to a doctor to have a check-up. He was sad and crying all the time." By the standards of other poor Palestinian families, Hanan's father was a remarkably kind man. Still Hanan's mother and brothers and sisters knew nothing of her plight.

"I discovered I was pregnant when I went to the doctor. Both my father and I were very fearful. Both of us were scared of my brothers and how they would react. I was most scared of the youngest, who is 24, a typical Jordanian guy, easily angered. So we left our place and moved elsewhere in Amman without telling the rest of the family. I tried to do an abortion by drinking anything I could find. I got many medications, but they didn't work. We tried to find someone who would do the abortion but we didn't know anyone. Days were going by – and it was obvious I was pregnant. All the time, of course, the family were trying to find us."

Hanan tried to travel to Egypt with the help a friend of her father's, a Lebanese man who was also blind and who suggested sending the young woman to Lebanon but there was fighting in Beirut. They wanted to obtain a passport for Hanan but the Lebanese man became ill and by then Hanan was six months pregnant. A doctor eventually came to her home and told her of the shelter run by the Jordanian Women's Union. She was immediately brought to the house where other women in fear of their families are cared for by volunteers and lawyers, a special section of the building cordoned off with a locked iron gate for those most in danger.

"I thought I would have the baby and then give it away," Hanan says. "The women helped me even though I wanted to give it away. But deep inside me, I wanted the baby. I couldn't say that to my father because we didn't know the identity of the man who raped me. But I knew this man was from the same neighbourhood and there was a neighbour of ours whose son knew the rapist's name.

"While I was in the shelter, the women tried to convince me to keep the baby. My mind was in conflict with itself. But when I delivered my baby, it was a different day to anything else in my life." Here Hanan's eyes lit up, independence amid adversity. "You know, you can say you don't want a baby, but you do. I was crying and scared that someone was going to say they would take the baby. And I was scared to say I wanted to keep my little boy."

Under Jordanian law, a women's shelter must inform the police if a child is born without the presence of the mother's family. When the cops arrived, they were polite but put a policeman on guard outside her door and grilled Hanan until six in the morning. "They made me feel like I was guilty," she says. Hanan told them all she knew about the rapist and about her father, who then told the police of the neighbour's son. When they showed the boy a set of photographs of criminals, he immediately identified the man who had raped Hanan. She recognised him too. The man, who had a long crime record, was already in prison for attempted murder. The police took Omar away to register his birth in a social services office but he was returned to Hanan who then moved to a government home. Yet her problems were far from over.

"The lawyers at the shelter knew of the danger to me and asked if I wanted to get engaged to this man – then I could get married and later divorce him – and tell my family that my 'honour' was intact. I could say I got married, had a child and then legally divorced my husband. The lawyers went to my rapist to arrange our marriage. He was still in prison and denied he had done anything to me. Then he agreed he had taken me – but said it was consensual! But eventually he confessed and signed a paper saying that I could do whatever I wanted with my baby. He also agreed to marry me.

"So a day came when my father and I went to court and we saw the rapist passing us with some policemen. But when we got married, on 20 October 2008, we didn't see each other. At this point I could keep Omar. I stayed in the shelter for a month after we were married. Everything was legal. So I went back to my father's place and we had a normal life. I kept visiting the Women's Union; they were trying to get a birth certificate for the baby and this took a year. The rapist – yes, the man I married – is now out of prison." Hanan has just told her mother and sisters of her ordeal. Her brothers still know nothing.

"I have told them I work in an orphanage, looking after children," Hanan says. "When I go to see the family, I take Omar with me and say he is a boy from the orphanage. They believe he is an orphan who is attached to me, but my brothers keep asking questions. Why is the boy with me all the time? Where is his family? They see him every two weeks or so and keep asking. Later, when I am divorced, I will tell my brothers the whole story. I think they will accept it. I will tell them that the union helped me and that everything is now legal. My mother and my sisters accept it, although they are sad. It was my father's idea that we should tell my brothers after I'm divorced."

Hanan smiles, more in hope than from conviction, I suspect. The women who helped her are also heroines, but they too are still concerned for her. "Without the Women's Union, if these people hadn't helped me, I would be dead – dead financially, dead psychologically and dead physically", Hanan says. "But God didn't want life to be unfair to me. Now the story has ended, thank God."

Hanan plans to tell her brothers – once she is divorced – that her former husband is in prison for raping her, that legal justice has been done, that she was married to him, that she divorced him, that "honour" has been preserved. But the brothers will know, of course, that she was raped before her marriage. Will this satisfy family "honour"? Hanan has fought her first battle – she decided to keep Omar – and now faces a much more serious one. Not that Omar would understand. The two-year-old struggles down from his plastic chair and demands chocolates. But given his mother's painful struggle, what world has he been born into?