Feb. 2, 2012  -- The scars of childbirth were still healing on Amelia Reyes Jimenez's stomach in 2008 when police came to her Phoenix apartment and took her three-month-old daughter from her arms.

Three and a half years later, Reyes Jimenez and her four children have become statistics in the U.S. crackdown on illegal immigration. Each year thousands of children of undocumented immigrants, like Amelia's kids, wind up in foster care when their parents are arrested for immigration violations. Some are even adopted by U.S. citizens while their parents are held in federal detention centers or deported back to their native countries.

Reyes Jimenez's son and three daughters are now living in foster care in Phoenix, and are awaiting possible adoption. Reyes Jimenez is back in Mexico, her parental rights terminated by an Arizona judge, and she cries when she remembers the raid that began it all.

"My daughters were calling, 'Mommy, my Mommy,'" said Reyes Jimenez. "I felt destroyed. I felt like I would never see my girls, even worse [the baby] was so small. I had just bought her cradle and her stroller."

WATCH: ABC News' Interview With Amelia

A new study by the human rights group Applied Research Center estimates that as of summer 2011 there were at least 5,100 children of detained immigrants in foster care in 22 states.

"It's clearly a systemic problem," said Rinku Sen, executive director of ARC. "It happens again and again and again in multiple states, multiple counties, different ICE agents, different detention centers, different judges." Though the report did not say how many kids had been adopted, ARC did find that detained parents were at risk of permanent separation from their kids because of deportation.

"It's sort of like saying, okay, you came here as an undocumented immigrant, we're going to break up your family, we're going to keep your kids," said John De Leon, and attorney who represents the Guatemalan and Mexican consulate in immigration cases. He says he has seen the issue grow into a national problem over the last decade.

WATCH a "Nightline" report on kids taken from moms.

PHOTOS: Tug-of-Love -- Kids Taken from Moms

The police came for Amelia Reyes Jimenez in 2008 to arrest her for one count of child endangerment, a misdemeanor, because she had left her 13-year-old son Cesar, who is severely disabled, alone in her apartment. Jimenez says she thought that Cesar was with her two older daughters and their father, but he had taken the girls to the park and left Cesar home alone.

When she arrived home with baby daughter Erica in her arms, she found the police waiting.

"The only thing they asked was if I was illegal and whether or not I had my papers," she said. She told them she had no papers. She was handcuffed.

Reyes Jimenez was sent to a detention center an hour outside Phoenix. It would be six months before she had any contact with her children, and nearly two years before she would see them again in person.

"I didn't know anything about my girls; they didn't give me any reasons," she said. "I would ask about them and nobody would answer."

Reyes Jimenez, who pled guilty to the misdemeanor, then spent nearly two years fighting deportation. Ultimately, she was loaded onto a bus and dropped off in Nogales, Sonora, Mexico, just across the border.

"It's very sad, very horrible because you're living a life, and then you come here and it's very strange," she said. "I feel empty without my children."

'I Don't Think There's Any Salvaging This Case'

Since then, she has been living outside Guadalajara, Mexico, with her sister, working nights on a factory assembly line making cell phones. She sleeps a few hours each morning in a borrowed bed and then waits by the phone in the corner.

She has to be there, she says, in case her lawyer calls.

Long after her deportation, Reyes Jimenez continued to fight two cases in the United States -- one in immigration court and another in family court.

Reyes Jimenez's three daughters are U.S. citizens. Reyes Jimenez and her attorneys spent two years trying to convince an immigration judge that she qualified for a visa on account of the harm that would be done to her three U.S. citizen children if she were to be deported. They lost -- twice.

That case is now being appealed to the Ninth Circuit Court of Appeals, but there is no trial date in sight and little chance of success, explained Nina Rabin, an attorney with the University of Arizona's Immigration Law and Policy Program who represents Reyes Jimenez.

"I don't think there's any salvaging this case," Rabin said.

"But, meanwhile, all of this took time," she said -- time during which the child welfare system had to make decisions about the children.

There are strict time-lines in place to ensure that children in foster care are placed in permanent homes sooner rather than later, said Rabin. If Reyes Jimenez hadn't been kept in detention for two years, Rabin believes, she would have had a much better chance of keeping her kids.

Rabin released a report last year titled "Disappearing Parents" that focuses on Amelia Reyes Jimenez's case. It details the way in which parents like Amelia can slip through the cracks between two huge bureaucracies: the child welfare system and Immigration and Customs Enforcement.

There are no policies in place, she says, to coordinate between the two systems. Caseworkers don't know how to find a parent in detention. Parents in detention are rarely released to attend family court hearings. They would be better off in jail, according to Rabin, where caseworkers know how to find you, jail personnel know where to send you and parents can meet the strict time-lines laid out by the family court.

In order to be reunified with their children, most parents will be given a plan to follow. They need to attend parenting classes, court hearings and show an effort to be part of their children's lives to prove they are fit parents.

But the family court in Reyes Jimenez's case listed in the record that "no services [were] available, due to mother's incarceration," according to Rabin. In detention, she had no way of meeting any of the court's usual requirements, so the court didn't give her any to meet. And, soon enough, it was too late.

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"It really puts parents in this terrible position of having to make a choice," said Rabin. "Do I fight my deportation and risk the clock ticking and facing termination of parental rights? Or do I take the deportation and try to fight from Mexico, or wherever I'm from, to get my child back?"

An Arizona court terminated Reyes Jimenez's parental rights in late 2011. The most recent publicly available information indicates that the children, who now no longer speak Spanish, are in foster homes and are in the process of being adopted. But Reyes Jimenez says she is determined to see her children again, to be their mother again.

"I'm not going to be satisfied until I'm back with them," she said.

ICE Memo: Don't Detain Caregivers for Handicapped

In 2009, while Reyes Jimenez was already in detention, the Obama administration announced it would address problems within the country's rapidly expanding immigration detention system. Since then, Immigration and Customs Enforcement has been clear in its priorities: criminal aliens and those who pose a threat to national security should be detained and deported first.

In June of 2010, ICE released a memo that said immigration officers are encouraged to consider a person's "family relationships" in the country when deciding whether or not to prosecute a deportation case.

In a statement to ABC News, ICE spokesman Brian Hale said that, "as outlined in the agency's June 2010 Civil Enforcement Priorities memo, ICE will typically not detain individuals who are the primary caretakers of children, unless the individual is legally subjected to mandatory detention based on the severity of their criminal or immigration history."

READ the full ICE statement.

The 2010 memo also said officers should consider whether the person has children who are U.S. citizens and "whether the person is the primary caretaker of a person with a mental or physical disability." Particular care should be taken in cases concerning "pregnant or nursing women."

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This is the second story in a series from the Brian Ross Investigative Unit's 2011 Carnegie Fellows, five student journalists who initiated and led a reporting project on the impact of the federal government's enforcement of immigration law. Read the first story here. The journalists are Lauren Gilger, Charles Gorra, Josh Haskell, Robin Respaut, and Selly Thiam.

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