Kira Cochrane talks to filmmaker Lisa F Jackson on her documentary about rape in the Congo

In a long conversation, the only time that Lisa F Jackson falls quiet is when I ask which moment most affected her in the making of her film The Greatest Silence: Rape in the Congo. Was it meeting a teenager, Immakilee, raped by soldiers and left pregnant at 15, who, as Jackson says, "has eyes that look like the world has abandoned her"? Or hearing the story of 42-year-old Marie Jeanne, whose husband was beaten and killed and, as she explains in the film, cut "into three parts, the head, the chest, and the bottom part ... then they raped me and abandoned me there. I passed out next to my husband's legs"?

It could have been meeting the four-year-old, raped by a man in her village, whose eyes, like Immakilee's, seem to have widened permanently. Or encountering the woman who stands up at a gathering, and gives, as Jackson says "the most unbelievable monologue I've ever heard" about women being raped, and forced to miscarry, and to "drink the blood from [their] wombs". In the decade-long conflict in the Democratic Republic of Congo, an estimated 5.4m people have died, and 200,000 women have been raped. "In the little village that I went to," says Jackson, "they would appear at my door, lining up before breakfast, wanting to talk. Sometimes I would videotape them when there was no light; I couldn't even get an image. And still they would be waiting in line."

Jackson's film tells both sides of the story. She sought out rapists, and found herself - a slim woman in her late 50s - pointing her camera at men who looked entirely ordinary save their guns, who recounted having carried out five, seven, 20 rapes. "It's hard to keep a record," says one. "We stayed too long in the bush, and that induced us to rape. For an approximate number, maybe 25." While many of the women she interviews are racked with shame, the men who attacked them have none. It is a moral inversion, but typical of attitudes to rape worldwide. Jackson eventually decides that it was seeing these men melt back into the hills that affected her most. "Interviewing the rapists was ghastly," she says, "but the worst moment was when they left. They had just confessed to war crimes, to heinous acts, and I had videotaped it, and then they just sauntered off into the woods. I couldn't help thinking: where are they going, who are their next victims?"

Jackson had personal reasons for making the film, briefly revealed on screen. In 1976, while she was working in Washington DC, three armed men seized her as she was leaving the office. They "took me into an empty van and raped me", she says. "I didn't know what they were going to do when they pushed me into the trunk of the car and locked it; whether they were going to shoot me, drive somewhere and dump me. I busted through the tail-light to get out, and the moment when that trunk came up, it was like a tomb opening. They had just left me. After getting out of the car, I flagged down a cop car. I went to the hospital, and then went back to my apartment and had a hot bath and a shot of Jack Daniels, and by then it was dawn and I went to work. I was in complete shock for a long time."

Despite making composite drawings of the attackers and attending a few police lineups, no one was ever prosecuted. The attack made the front pages, and rather than being pleased at the spotlight, Jackson was appalled that so many other rapes passed unmentioned. Thirteen years later, she wrote an article for Newsweek in response to an attack in Central Park that had had massive press attention. "That same night in Central Park, three other women were raped," says Jackson, "and the fact that she got all the attention - I flipped ... I was just so angry that we cannot look at this crime - we cannot look at the number of women, we have to fixate on one, because it allows us to ignore the dozens of others. Why isn't every woman who is raped front-page news, like I was? ... War is always described from a male point of view. Male survivors of war have bragging rights. They get to write books, they get to be heroes, they get ticker-tape parades. And the women survivors of war have nothing equivalent."

Jackson studied film at the Massachusetts Institute of Technology, and she has since been involved in dozens of films, working on subjects as diverse as the symbolism of Barbie dolls and victim-offender mediation schemes. Her subjects have often been serious, but none other has led her to the kind of activism prompted by The Greatest Silence. It is clear that Jackson is on a mission - that she is determined that these women, who have horrific injuries but barely any medical provision, who have no chance of seeing their attacker prosecuted, who are, in almost every case, abandoned by their husband because of the "shame" of the attack, have representation.

"I feel really passionate about using the film as an advocacy tool and, in some situations, as a bludgeon," she says. "The Foreign and Commonwealth Office of your very own government has paid to have the film translated into Swahili and Lingala, and they are going to buy time on Congolese television ... I've screened it in the US Senate, I've testified to the Senate, I've screened it in the House of Commons, I've screened it in the Belgian parliament, in the European Commission. We're going to screen it in the Hague. It's important that governmental agencies, and governments, see it, and that individuals become aware of it."

When Jackson began filming in the Congo, she was expecting the material to become part of a larger film on the experiences of women and girls in conflict. She soon realised that the story stood alone. She is continuing with her theme in her next project, a documentary set in Bogota, Colombia, following women who are "internally displaced - have been kicked off their farms, or out of their towns, by either the paramilitaries or the Farc".

For many years she tried to make a film about the "very brilliant" sex crimes unit in the New York City Police Department, and tells me the story of one of the detectives who, after 15 years in the department, was transferred to homicide. "He described the going-away party that the sex crimes detectives gave him, and one of them said, 'You're going to the big time, you're going to homicide.' He said, 'I've been working homicide - that's what rape is: murder of the mind.'

Besides killing, it's the worst thing that someone can do, because you're forced to live with it." In Jackson's case, at least, that experience is being put to some use.

· The Greatest Silence: Rape in the Congo will be screened at 4.30pm on May 11 at the Frontline Club, 13 Norfolk Place, London, W2 1QJ. To book, go to frontlineclub.com or call 020-7479 8950.

· This article was amended on Monday May 12 2008. In the standfirst we mistakenly said the assault had taken place in New York when it was in fact Washington. This has been corrected.