áine Fryers was 16 when her father was arrested with Semtex in London. He was incarcerated along with other IRA prisoners in Belmarsh high-security prison.

"You seen other visitors going in and being searched and it was just a wee rub down. But if you were Category A, they nearly tore you apart, checking through your clothes and right up your leg and you could see the other people looking and going, 'God, they must be dangerous.'"

There were five children in áine's family and the cost of travelling to England meant visits were few and far between. "You went into a wee room and there was a table in the middle and a chair this side and one chair that side and that's where my daddy sat, and a screw then sat behind him so you couldn't really talk. If you wanted to tell him you loved him you were too embarrassed to because there was someone else in the room. Leaving him was really hard because I knew I wasn't going to see him for another year."

Over the course of the Troubles, some 30,000 people were jailed as political prisoners. That figure has given rise to estimates of around 100,000 children and young people affected by the incarceration of a parent. They experienced poverty, isolation, prejudice and stigma, as well as a sense of bereavement. The vast suffering represented by more than 3,700 deaths and 40,000 injured has tended to overshadow the emotional damage wrought by the conflict. Despite their obvious pain and hardship, children of paramilitary prisoners have had to share the burden of society's condemnation of their parents, so have received little public sympathy.

After initial reservations, áine Fryers came to wholeheartedly respect her father's decision to join the IRA. "I resented the IRA for a while at first, thinking they took him away and now he's going to be in jail for a long time and it's their fault. But then I spoke to him and realised he did it for us and for his community and I thought fair play to him, he made the decision himself to join the IRA and he did what he had to do for us and for his family."

In the North's most troubled neighbourhoods, the prison experience was ubiquitous and travelled down generations. Liz Rea lives in the Shankill and is the daughter of Gusty Spence, a former leader of the UVF. He went to prison in 1968, when she was just 12. "My daddy was sentenced to 20 years and God bless my mummy, she waited 19 years on him. Never in all my life did I hear my mummy criticise my daddy for going to jail – never. And she reared four of us on her own," she remembers.

Five years into her father's sentence, Liz married another loyalist paramilitary fighter who was to serve a long jail term for his activities. She was left to raise their son alone. "We were married on 1 July and my husband was arrested in February. I was eight months pregnant at the time and I was 18 years of age. My son was born in August and the day I got out of the hospital the first thing I did was go to the chemist and buy him a dummy and went straight to the Crumlin Road jail to let his daddy see him. And then the following day he was taken to Long Kesh to see my daddy. That was the first couple of days of his life."

It was common for children to be told their fathers were "working away". "I told him his daddy was building houses," says Liz. "I says, 'Your daddy's in there building houses along with your grandda.'"

If having a parent in prison was difficult, having him home again could be even more problematic. John McComb's father joined the IRA and was arrested while digging up an arms cache on the coast of Wales.

"When my daddy was released we had Christmas dinner together for the first time I could remember, and I was 16 so I was allowed to drink a beer and then had two beers!" says John. "But he tried to ground me and I just completely ignored him because he wasn't about for 11 years."

Liz's son, who had no memory of his father living at home, found his return disturbing. "For the first week he wouldn't let us sleep because he didn't want his daddy in that bed. 'What is that man doing in your bed Mummy?' He couldn't get to grips with why there was a man in my bed."

As well as the emotional issues, adult children of prisoners continued to face social stigma and some very practical restrictions on their lives. áine had to apply for a visa to go to Canada with a youth group. "The form said, 'have you or any other member of your family been convicted of a criminal offence in the UK or any other country?' And I said no. And the girl we were going with said, 'but your daddy's in jail'. And I went 'yeah, but he's not a criminal, he's a political prisoner.' So that's how I got round it."

áine neatly sums up the situation for children of political prisoners: "I'm told I'm not a victim of the conflict because my parents didn't die and because my father chose to join the IRA and was arrested. But as far as I'm concerned I am a victim of the war. People say, 'How can you say you're a victim? Your father chose to do it.' But I didn't choose to do it. I was just there, I was born into it, it wasn't my choice for my daddy to join the IRA.

"And that's what needs to be recognised – that you can't just pick and choose who victims are."

Laura Haydon's documentary Sins of the Fathers was broadcast on Newstalk 106-108FM yesterday