UPDATE, July 31, 2014: This story updates to include a newly released inspector general's office report.

The child immigrant crisis on the southern U.S. border had been at the top of the news for weeks, but less attention has been given to what happens to the children immediately after U.S. Border Patrol agents seize them. The Center for Investigative Reporting, which has covered border issues extensively, has put together an FAQ to explain what happens to those children between the time they’re apprehended and the time they’re put into the system.

What responsibilities does the Border Patrol have?

The priority mission of the Border Patrol is preventing terrorists and dangerous people from entering the United States. But Border Patrol agents also are frequently the first responders for immigrants without authorization to enter the country – including children entering without parents.

The Border Patrol is responsible for the apprehension, temporary housing and preliminary screening of these children before they move to long-term housing, where they await immigration processing.

More than 57,000 unaccompanied children have crossed the U.S.-Mexico border since October. More than half of them fled Central America because of gang violence and domestic abuse, according to a United Nations report released earlier this year.

That number is double that for the same period a year earlier, prompting concern among lawmakers about what to do with the children, where to house them in the meantime and whether the U.S. can afford to care for them.

But before the children reach a shelter to await a hearing, they must make another journey through a complex and trying Border Patrol processing system.

Where do these children go when Border Patrol agents apprehend them?

The first stop for anyone caught coming into the U.S. illegally is a Border Patrol station. Each station has cells where immigrants are held until they can be processed and released or transferred to a long-term facility. Unaccompanied children are housed separately from adults. As CIR reported last year, these holding cells often are known as las hieleras, or “the freezers,” because they are so cold that immigrants sometimes get sick or leave with cracked skin.

Complaints to the U.S. Department of Homeland Security’s civil rights office describe poor conditions, including lack of medical care, insufficient food and water, and incidents of verbal and physical abuse. Because the holding cells are meant to be temporary, many do not have soap, showers or beds.

The inspector general's office released results today from its review of dozens of Border Patrol sites and ports of entry. While the inspectors found temperatures as low as 56 degrees at some stations, they reported that most facilities complied with Customs and Border Protection policies on factors such as availability of meals and water, and supervision of children. The review was prompted, in part, by a June complaint by the American Civil Liberties Union alleging mistreatment of 116 unaccompanied migrant children.

By law, children cannot be held in Border Patrol stations longer than 72 hours. But some are held for as long as a week before they are moved to shelters or returned to their home countries.

“We have increased our capacity, but the number of children coming in has increased as well,” W. Craig Fugate, administrator of the Federal Emergency Management Agency, said at a U.S. House of Representatives hearing on the crisis in June. “We have not reached the 72-hour mark.”

Are these conditions due to the influx of children?

U.S. Customs and Border Protection, the Border Patrol’s parent agency, told NPR in a recent report that the poor conditions in holding cells are due to the recent inundation of unaccompanied minors. But complaints filed with the Department of Homeland Security suggest that such conditions have existed for years.

Summaries of complaints about the treatment of immigrant children from 2005 to November 2013 note numerous instances of mistreatment of minors and poor conditions in holding cells – well before the current crisis started. Such complaints must be filed when children tell intake workers from the Department of Health and Human Services that they were mistreated. The department’s Office of Refugee Resettlement takes custody of the children after the Border Patrol processes them. The office is responsible for the care and placement of unaccompanied children while they move through the immigration system.

In a 2006 complaint, a 17-year-old boy from El Salvador said he and others were fed only twice a day and their only water was from a toilet tank. “He also alleges that the cell was very cold, that they were not provided with blankets, and that the detainees had to sleep shoulder to shoulder to stay warm,” according to the complaint.

A 2007 complaint alleges that agents kicked two youths so badly they had to be taken to a hospital. It also said “their food was thrown at them, and they were cold in the holding cell and not provided blankets.” A worker from the Office of Refugee Resettlement noted that one child had cuts on his chin and lip and was never given his prescribed medication.

How are the children screened?

When children are apprehended, Border Patrol agents ask them a series of questions to determine whether they are victims of persecution or human trafficking and therefore eligible for protection in the U.S under asylum laws.

But advocates say the brief screenings are not effective because agents are not trained to deal with children – especially children who may have experienced trauma. In addition, Border Patrol stations are intimidating – not the kind of place where children or teens are likely to feel comfortable talking about kidnapping or abuse. And interviews often are conducted in the open.

If the children are from Mexico, this may be the only interview they get. Under the 2008 reauthorization of the Trafficking Victims Protection Act, if the Border Patrol determines children from a country contiguous to the U.S. are not at risk of being trafficked or persecuted, they can be sent back immediately.

But a confidential U.N. report first obtained by the news website Vox says the Border Patrol is returning Mexican children who may be in danger at home because many agents don’t understand what to look for in the screening process.

“In general,” Vox quoted the U.N. report as saying, “CBP’s style of interviewing Mexican unaccompanied alien children seemed to focus on producing quick answers rather than substantive ones.”

Central American children, on the other hand, are transferred to the Office of Refugee Resettlement, where they receive more thorough screenings by trained workers.

Shouldn’t the Border Patrol have been better prepared?

Last year, a research team predicted that the Border Patrol soon would be overwhelmed and warned the White House that the federal government didn’t have the capacity to handle a growing influx of immigrants, The Washington Post reported.

A CIR investigation published in November found that about 730 immigrants were being temporarily housed in a Border Patrol facility meant for 250.

In interviews with CIR, Border Patrol agents said they have been frustrated with the lack of resources, and the influx of children this year only highlights the problem to the public.

The Border Patrol union has been outspoken on Twitter, retweeting photos of crowded cells and posting a story about agents using their own money to buy diapers for young children in custody.

“New annual job rating areas: Babysitting, Diaper Changing, Burrito Wrapping, Cleaning Cells. Law Enforcement? What’s that? #lowmorale,” the union posted in June, according to news reports. The tweet has since been deleted.

What’s being done to help the Border Patrol and improve conditions inside?

In June, FEMA began to coordinate housing, transportation, care and medical treatment among the various federal agencies involved, including the Border Patrol.

The Border Patrol recently opened a central processing center in McAllen, Texas, with a capacity of 1,000. The facility will help ease overcrowding and reduce the need to fly and bus children to the main processing center in Nogales, Arizona, reducing the time they will potentially spend in Border Patrol custody.

The White House requested $3.7 billion in emergency funding to address the surge, $364 million of which would go to Customs and Border Protection for temporary housing, screening and related care costs for unaccompanied children, as well as overtime pay for Border Patrol agents. Senate Democrats are moving forward with a $2.7 billion package, and House Republicans have put forward a $1.5 billion package, according to a recent Washington Post report. Customs and Border Protection will likely run out of funding by mid-September without emergency measures, Homeland Security Secretary Jeh Johnson told the Senate Appropriations Committee this month.

The surge in unaccompanied immigrant children has slowed in recent weeks, with apprehensions hovering around 500 unaccompanied children per week in the busiest Rio Grande Valley sector, down from the peak of up to 2,000 per week in June.

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This story was edited by Jennifer LaFleur and copy edited by Nikki Frick and Christine Lee.