He was only 5 when he saw his mother and younger brother killed and the soldiers took him away to their base in a helicopter. She was just 6 when she was separated from her parents during a bombing raid and delivered to an orphanage here.

Amilcar Guardado, who is about to turn 22, was raised by military officers on an air force base. Imelda Lainez, now 17, ended up being adopted by a family in the United States, where she was given the name Gina Marie Craig.

Now, both have been reunited with their original families, beneficiaries of a private investigative program that has forced El Salvador to confront one of the darkest secrets of its civil war, which lasted from October 1979 to January 1992.

Some 75,000 people were killed in the war -- most of them by troops trained and financed by the United States -- or disappeared and were presumed dead.

Among those who disappeared were hundreds of children who, parents and human rights groups say, were kidnapped by the Salvadoran military during attacks on peasant settlements suspected of harboring guerrilla fighters or sympathizing with the leftist insurgency.

''These children were robbed, abducted in the countryside by the military for a variety of motives,'' the Rev. Jon de Cortina, a Spanish Jesuit priest who is the founder of the El Salvador Disappeared Children's Search Association, said in an interview at the group's headquarters here. ''But we believe that their right to recover their identity, and the right of their families to know the fate of the children they lost, must be fulfilled and respected.''

Since its founding in 1994, the Children's Search Association has registered what it says are 323 instances of children who were taken by army troops or separated from their families in battle zones.

But the group has barely begun working in some areas that experienced heavy combat and expects at least 500 cases to be uncovered before that task is complete. So far, there have been 29 reunions of children with their parents.

Though most of the missing children appear to be in El Salvador, where the military placed them in orphanages or with new families, nine have been located in the United States, Italy and France. To help match parents and children, Physicians for Human Rights, a group based in Boston, has conducted DNA tests on both.

But reunification has not been easy. Records have disappeared, some orphanages and family court judges have refused to cooperate, and the Salvadoran military has discouraged efforts to link the disappearances to massacres and military offensives or to investigate the possible trafficking in kidnapped children.

In contrast to its stance during the war, the United States Embassy here now says Salvadoran officials engaged in ''clear-cut fraud in certain instances'' in which children here were adopted by American families.

There are no reliable statistics on how many of the 2,300 Salvadoran children adopted by Americans during the war may have come from the pool of abducted children, but there has been no suggestion by anyone involved that adoptive American parents acted in anything but good faith or that more than a small percentage involved abducted children.

''We were dealing with a Government agency, courts and our own embassy, so we just assumed everything had been checked out,'' Thomas Craig, Gina's adoptive father, said in a telephone interview from his home in Ohio. ''Here we have been trying to build a relationship, and now we find that the whole cornerstone of it is built on a lie.''

Abducting Children As a Tactic of War

Gen. Humberto Corado, the Salvadoran Defense Minister, has rebuffed efforts to obtain a public accounting for the missing children.

Last year Gen. Adolfo Blandon, a former military chief of staff and Defense Minister, acknowledged that families had been separated during the war but attributed the military's conduct to humanitarian motives.

''During the war, there occurred cases in which children were found in war zones in situations of extreme danger and evacuated to the sites of different units,'' he said. ''Some were handed over to welfare institutions, others given to the care of some families, while others remained under the responsibility of the unit that evacuated the zone.''

Others tell a much different story. Taken together, their accounts suggest that some children were abducted to prevent their later incorporation into guerrilla groups, others to intimidate families sympathetic to the insurgents and a few to serve as mascots or trophies of war or even to be sold for profit.

Miss Craig, for instance, remembers being with her parents, who acknowledge they were rebel supporters, and two sisters when a bombing raid began one day in 1984.

Wounded by shrapnel in the attack, which killed her older sister, Vilma, she was evacuated to a rebel field hospital. Days later, she was taken away by soldiers during an assault that left no other survivors.

Miss Craig was wounded in her right leg. At the orphanage, where the soldiers left her, she was put in a wheelchair. But after the Craig family adopted her, she was operated on and is now an avid basketball, softball and volleyball player.

''The emotion is very great,'' said Jose Lainez Ayala, 40, Miss Craig's biological father. Mr. Lainez, a farmer, was re-introduced to her last week when Miss Craig visited the poor village of Los Cocos, where he and his wife, Miss Craig's mother, Victoria, live.

''You can't imagine what it is like to lose a loved one,'' he said. ''This fills the vacuum we had in our hearts.''

Not a day went by during the dozen years she was missing, Mr. Lainez added, that he did not wonder whether his daughter was dead or alive.

''This is like awakening from a nightmare that I thought would never end,'' he said.

Years of Alienation And Resentment

For Miss Craig, and both of her families, there is now peace. Miss Craig said she is planning to finish high school and attend college in the United States, but hopes to visit her family here regularly and eventually to assist them financially.

''We were able to heal her of her war wounds, to educate her and to bring her up in the faith of the church,'' Tom and Stephanie Craig wrote in a letter to Jose and Victoria Lainez, expressing their happiness at the way things have turned out. ''But we were never able to mend her broken heart.''

But not all the family reunions have had such a happy ending. The first words that a dazed and distant Juan Carlos Serrano uttered to his mother after 12 years of separation, workers from the Children's Search Association recalled, were ''Why did you abandon me?''

Soldiers had taken the boy, named Nelson Ramos at birth, from the arms of his mother, Maria Magdalena Ramos, during a military operation in 1982 when he was only six months old, she said. As her child grew up in an orphanage, Ms. Ramos lived with the tormenting conviction that he had been forced into the army and might end up in a unit that would attack and kill her.

''In some cases, the abducted children were told by soldiers or Red Cross workers that they shouldn't cry, that their mothers would come for them soon,'' said Rosa America Lainez, a psychologist who works for the Children's Search Association and is not related to Jose and Victoria Lainez. ''So they sat in the orphanage each day, waiting for their mothers to return, until they had built up a resentment toward their parents.''

Though some of the children have fared better than others, ''the moment of separation has proven traumatic in all cases for everyone involved,'' whether child or parent, Ms. Lainez said. Some children, she said, can still recall seeing their parents killed before them. ''Always there are the same questions,'' Ms. Lainez continued. ''What happened, and why did it happen to me? Who am I, and where does my true path lie?''

For Amilcar Guardado and his brother Mauricio, 25, those questions are especially hard to answer. After their mother was killed in 1980, soldiers took the boys back to their barracks and provided them with food, shelter and an education, but not the warmth of a family.

''After the death of my mother, I became cold,'' Mr. Guardado said. ''The good side is that we learned things, and some of the officers would take us out on trips. But all we saw was wounded soldiers, how they, too, were poor guys who suffered in the war. There never really was true affection, nor any of the hugs and kisses that only a mother can provide.''

Today, Mr. Guardado and his brother continue to live at an air force base, where they work as helicopter mechanics. But they have re-established contact with their only surviving uncle and his children.

In an interview here, Gina Marie Craig said that when she began to feel estranged from her adoptive parents, she was sent to see therapists. Invariably, she said, they told her that the belief she had another family here was ''just a dream,'' a fantasy that needed to be overcome.

''All along, though, I had the feeling in my heart that they were still alive and out there looking for me,'' she said. As a result, ''I couldn't get along with anybody'' in the Akron suburb where she grew up so immersed in middle-class America that she lost her ability to speak Spanish.

''I was forced to come,'' she said of her adoption and move to the United States. ''I didn't have a choice. That's how I felt. I always saw myself as Imelda, not Gina.''

Questions Raised On Embassy Actions

Miss Craig's case has raised questions about how the American Embassy processed adoption petitions here during the war. In her own case, she said, American consular officials readily accepted ''a false birth certificate'' and a certificate of ''moral and material abandonment'' that had to be issued by Salvadoran courts for her adoption.

About half of the 2,300 adoptions of Salvadoran children by American families took place over four years in the mid-1980's, when fighting was most intense and families were most likely to be separated.

A spokesman for the American Embassy here, Chris Midura, acknowledged that ''there wasn't much procedure for checking up on these things during the early years of the war.'' But as the conflict went on, he said, ''and there was obviously fraud going undetected,'' the embassy ''starting around 1989 began investigating every individual case for veracity,'' and the number of adoptions dropped.

Recently declassified State Department documents indicate that the embassy here was aware of at least some irregularities. In them, a prominent Salvadoran death squad leader with close ties to the military is identified as ''having snatched babies from the conflictive zones in order to sell them for adoption.''