One day last spring, Fredy Peccerelli found himself conducting an unusual exercise: correlating the dates of major massacres during Guatemala's civil war to the play schedule of the New York Yankees in the 1980s. It was an attempt, the director of the Guatemalan Forensic Anthropology Foundation says, to compare what happened in his native country with his own life after he and his family fled in the fall of 1980 when he was nine years old.

The violence in Guatemala's 36-year insurgency peaked between 1980 and 1983, under the military governments of General Fernando Romeo Lucas García and General José Efraín Ríos Montt. Both regimes led scorched-earth campaigns in the Guatemalan countryside and "disappeared" urban intellectuals who opposed the government. By the time peace accords between the government and an armed resistance movement called Unidad Revolucionaria Nacional Guatemalteca (Guatemalan National Revolutionary Unity) were signed in 1996, 200,000 people had perished, many in massacres that targeted entire villages, according to the country's Historical Clarification Commission, a United Nations–led investigation into human rights violations there.

As a kid, Peccerelli knew that his family had fled to New York City because his father, then a law student, had received threats from government death squads in the capital, Guatemala City. "At that time, they were killing a lot of people at the law school," says Peccerelli. "[My father] had a lot of people around him disappear." So when the threats came, the family l quickly fled.

Peccerelli didn't ask many questions—and his parents didn't volunteer much information—about his native country as he and his siblings struggled to adapt to their new home in Brooklyn, N.Y. Instead, he focused on learning English, making friends, and on his favorite baseball team—the Yankees.

It wasn't until fall 1994, during his final semester at Brooklyn College, that Peccerelli began to learn the details of Guatemala's violent history. He attended a meeting of the American Anthropological Association in Atlanta, where he attended a lecture called "Excavating the Past, from Guatemala to Kurdistan" given by Karen Burns, a forensic anthropologist then at the University of Georgia in Athens and now at the University of Utah. Burns began her talk by describing the then-new Guatemalan Forensic Anthropology Team, called FAFG (after its name in Spanish, Fundación de Antropología Forense de Guatemala).

FAFG exhumes mass graves found in the Guatemalan countryside in an attempt to identify massacre victims—and how they died. The anthropologists analyze the unearthed bones for fractures, bullet holes, slash marks and other clues to causes of death. They compare the bones and other materials—such as clothing fragments—found in the graves with descriptions of the missing and the dead in the hope of compiling enough scientific evidence to identify and prosecute the victims' killers. When the work is complete, the researchers turn over the remains to victims' survivors so that they can have closure—and arrange proper burials for their loved ones.

After the lecture, Peccerelli spoke with Burns, who told him that she was about to lead a two-week forensic anthropology training course in Guatemala. Peccerelli was an anthropology major, but had not studied forensics; intrigued, he signed up.

When he completed the course, FAFG hired him as a forensic anthropologist, and he moved to Guatemala. It all happened so quickly that he took an incomplete in his final college class. (Two years later, he would complete the requirements through the mail to earn his bachelor of science in anthropology from Brooklyn College.) Over the next few years, his parents and siblings all returned to Guatemala, as well.

Peccerelli's first exhumation was in 1995 in a jungle town called Cuarto Pueblo, where he met survivors of a 1982 military massacre. He and his colleagues corroborated survivors' descriptions of the massacres by documenting where the soldiers had killed villagers and burned the bodies. "I slept a few feet from one of the pillars where [government soldiers] would slam the babies and kill them," he says quietly, clearly moved as he describes meeting massacre survivors.

It was a year before the peace accords would be signed, and government troops and resistance fighters were battling just over the next hill. As part of a program to repatriate refugees from Cuarto Pueblo who had been living in Mexico, the U.N. had an outpost on the hill overlooking the area where battles occurred. Sometimes at night, Peccerelli says, he and other anthropologists would climb the hill to the outpost to watch the fighting.

At the time, FAFG was a five-person team. In 2000 it became a foundation and Peccerelli was named executive director. Thanks largely to funding from the U.S., other foreign governments, and private contributions, he now oversees a staff of 90. The operating budget for this year is projected to be $3 million, although the organization will not hear back on some grant applications until next month.

The Guatemalan government provided $100,000 in 2006 and 2007 to the foundation, Peccerelli says, adding that local funds dried up after the current president, Alvaro Colom Caballeros, took office in January 2008. Peccerelli says the foundation's major backers are the U.S. Agency for International Development (USAID) and the Netherlands, which have each provided annual grants in sums between $500,000 and $1 million since 1999; last year, Sweden provided a similar amount.

Because most of the massacres occurred in the countryside and were targeted at indigenous communities, Peccerelli says many middle class Guatemalans, who are generally of Spanish descent, have largely ignored them. Gen. Efrain Ríos Montt, a former de facto president of Guatemala and army general, who human rights advocates say ordered massacres, was nonetheless elected in 2007 to a four-year term in Guatemala's congress, making him virtually immune to prosecution in the Guatemalan court system. Other former government officials believed to have played a role in the mass killings hold influential positions in the private sector, says Sebastian Elgueta, a Central America researcher with Amnesty International.

Jack McCarthy, who was a USAID program officer in Guatemala from 1997 to 2000 after the peace accords were signed, notes that most Americans are unaware of the scope of killings in Guatemala. USAID supports projects that promote postwar justice and reconciliation in Guatemala, and McCarthy, who is now a consultant with international development firm DAI (Development Alternatives, Inc.), was impressed with Peccerelli's efforts to grow FAFG. "I still remember writing the memo justifying [U.S. financial support for FAFG]," he recalls. "The demand for quality work and a strategic approach was so obvious."

In addition to investigating the crimes of Guatemala's past leaders, the anthropologists occasionally assist Guatemala's law enforcement agencies in tracking down forensic clues in crime cases. In one recent case involving the murder of a prison inmate, FAFG scientists found pieces of the victim's bones and other body parts in the prison's drain system; they determined that other inmates had killed him, and then cut up his body, cooked the pieces and ate them.

After the Bosnian War ended, Peccerelli and other FAFG anthropologists were part of the first team to exhume massacre sites there. Peccerelli returned for two more tours in Bosnia in the late 1990s, and in 2007 testified about the Srebrenica massacre (in which some 8,000 boys and men were slaughtered) at the International Criminal Tribunal for the former Yugoslavia.

"He's got one of the broadest perspectives on the application of forensic anthropology in all of Latin America," says Tal Simmons, a forensic anthropology professor at the University of Central Lancashire in England, where Peccerelli studied in 2003. "He's accomplished an absolutely phenomenal amount."

Last November, FAFG opened the first forensic DNA lab in Guatemala Funded by $1.8 million in grants from the U.S. State Department and the Dutch government, the lab will enable scientists to confirm the identity of the dead by comparing DNA isolated from bone fragments with DNA samples from surviving family members.

Peccerelli hopes the work will lead to criminal prosecutions of the soldiers and police who committed the murders as well as the leaders who ordered them to be carried out. Amnesty's Elgueta says that the "intellectual architects" of the most violent campaigns have thus far eluded prosecution.

In 2005 Spain's constitutional court (the county's highest court) allowed 1992 Nobel Peace Prize–winner Rigoberta Menchú Tum, a Mayan Guatemalan woman and famous resistance organizer, to pursue a case against former Guatemalan dictators Ríos Montt, now 82, and Lucas García (who died in Venezuela in 2006), three former generals, and two civilians under the principle of universal jurisdiction, which allows cases against perpetrators of crimes against humanity regardless of the nationality of victims and defendants. FAFG's work could be used in cases such as this one. Because of Rios Montt's position in congress, Elgueta says, it is unlikely he would be extradited, but the case carries symbolic value. So far, the seven defendants have been charged, and investigators are pursing the investigation; a trial date has not been set.

Peccerelli hopes the new lab will renew interest in the conflict within Guatemala, by allowing the foundation's scientists to focus on a new class of victims: the "disappeared," an estimated 40,000 intellectuals from Guatemala City—including some of Peccerelli's father's law school classmates—who vanished during the civil war and are believed to have been kidnapped and killed by government death squads.

Archives from the country's former National Police, which were discovered in 2005 by workers from the government human rights office in a crumbling Guatemala City warehouse, show that many of the disappeared were killed and their remains dumped at city graveyards  marked "unidentified," Peccerelli says. He plans to exhume those remains and compare their DNA to samples from surviving family members.

One major challenge remains: convincing the families of the disappeared to come forward. Amnesty International records hundreds of attacks against human rights activists each year in Guatemala, and a 2007 UNDP (U.N. Development Programme) report identified Guatemala as "one of the world's most violent countries." Many Guatemalans whose family members were killed by the death squads still live in fear themselves.

This is something Peccerelli, now 38, understands all too well. He began receiving death threats in 2002. The threats are anonymous, but he says they appear to be related to his work gathering evidence against former high-level government officials. A recent threat, however, has raised new questions. On January 8, he received an e-mail from someone threatening to kill his family, starting with his brother Gianni, 36. The message included a surveillance photo of his brother's car parked at a gas station near his home. Four days later, Amnesty International put out an action alert asking its members to write to the Guatemalan government requesting an investigation of the warning. On February 12, Guatemala's Minister of Government, Salvador Gándara Gaitán, who oversees domestic security, sent a letter to several Amnesty International offices stating that the threat was a hoax perpetrated by Gianni.

"We are supporting the investigation," says Peccerelli, his voice sounding strained as he describes the allegation against his brother. He says Gianni has denied sending the threat, and FAFG maintains that this and all death threats should be investigated by Guatemalan prosecutors, noting that this is the first time in seven years that officials have even claimed to have probed threats against FAFG staffers and their families. No one has been charged in this case and government prosecutors have not turned over any evidence to support the claim that Gianni Peccerelli was behind it.

"Fredy's position, telling them to investigate this, it's very honorable," says Amnesty's Elgueta, who notes that even if the allegation against Gianni turned out to be true, Amnesty is still concerned about past threats. Peccerelli says that FAFG's office has been hit by gunfire, most recently in May, when a shot was fired into the office after an afternoon accreditation ceremony. There were no injuries.

"The work we do threatens people's liberty and comfort," says Peccerelli. "For us at the Foundation, this is about changing the country."

The International Commission Against Impunity in Guatemala (an independent organization with international and Guatemalan staff formed in 2007 by an agreement between the U.N. and the Guatemalan government) says that some of the former government counterinsurgency forces and death squads continue to operate today as crime syndicates and that they operate with a large degree of impunity: Only 2 percent of the homicides that occur in the country each year reach trial.

Peccerelli hopes FAFG's work will help efforts to end that culture of impunity. Despite the threats, he says, when he recalls his family's flight from Guatemala in 1986, it strengthens his resolve to stay and see his work through.

"I've sort of made a promise to myself," he says. "Whenever I leave it's going to be on my terms—because I want to."