"I spent 32 years living a lie," he says.
Mr Madariaga, 33, used to be called Alejandro Ramiro Gallo, the name given to him by his adoptive parents.
Francisco Madariaga says he always doubted his origins
Last year he came face-to-face for the first time with his real father and confirmed his fears.
He is the son of one of thousands of left-wing activists who were tortured and killed during military rule in Argentina between 1976 and 1983, a period known as the Dirty War.
'Systematic plan'
"For decades my captors [as he describes his adoptive parents] told me I was their biological son. But lies can't last forever," says Mr Madariaga.
The fate of Argentina's "stolen babies" has been back in the headlines this past week, with the start of the trial of key members of the former military junta on charges of operating a systematic plan to take babies from pregnant detainees.
Eight people are on trial, including former leaders Jorge Videla and Reynaldo Bignone.
The accusation against them relates to 34 children who were allegedly stolen. But it is estimated that hundreds of children were given away to members of the security forces, and in some cases to the same captors of the jailed activists.
Mr Madariaga's supposed "father" was Victor Gallo, an intelligence officer at the clandestine detention centre at the Campo de Mayo military base.
He was handed over to his new "mother" only a few days after his real mother was forced to have a caesarean at the military base.
Route to discovery
The lack of resemblance to his new family made Mr Madariaga suspicious of his origins over the years.
"It is something difficult to explain. It's like I always knew something was not right," Mr Madariaga says.
Mr Madariaga says he was regularly beaten by his adoptive father, abuse that reinforced his doubts.
"I think I was like a prize of war," Mr Madariaga says.
It was only last year that he confronted his "mother", who is now separated from her husband, about his real origin.
When she revealed what had happened, Mr Madariaga approached the human rights group, Grandmothers of Plaza de Mayo, who helped him have a DNA test that confirmed his true identity.
But the group's biggest help was to arrange a meeting between Francisco and his biological father, Abel, who had fled the country during the military rule.
"It was the best moment in my life. I couldn't believe how much I looked like him," says Mr Madariaga.
Francisco was labelled "Grandson 101". The number represents the amount of adults with similar stories who have now, after many years, regained their identities.
Human rights groups believe there could be some 400 people in the same situation.
Contact severed
But not everyone wants to know the truth.
The trial is expected to last several months
Finding out that your parents colluded in the atrocities committed by the military government is something some choose to ignore.
One well-known case is that of Marcela and Felipe Noble, whose adoptive mother is the owner of the newspaper Clarin, one of the biggest media groups in Argentina.
They were adopted in 1976, the first year of the military government, and now two separate families are seeking through court to prove that they were taken from their imprisoned relatives.
However, Marcela and Felipe have publicly expressed their trust in their adoptive mother, saying there is no evidence against her.
"I can understand those who don't want to know," says Mr Madariaga.
"For some, it takes more time than for others. Every case is different", says Rosa Roisinbit, a member of the Grandmothers.
In 2001, after years of investigation, she finally found her missing grandson who lived under a different name.
"However, the truth has to be above everything," she says.
"Some of the people who regain their identities don't want to know anymore from their adoptive parents. Others keep in touch", says Ms Roisinbit.
In Mr Madariaga's case, he severed all contact with his "father" and says he looks forward to seeing him in court.
His adoptive father, Victor Gallo, the former intelligence officer, was arrested last year. He is expected to testify, as part of the trial that is currently focussing on Videla and Bignone but which is expected to include many more people accused of kidnapping babies.
Mr Gallo's side of the story is that he was a training officer and that baby Francisco was given to him by chance by a superior officer.
"It is all lies", says Mr Madariaga.
"And lies cannot last forever."
By Vladimir Hernandez
BBC Mundo, Buenos Aires