Walther told the parents following her ruling they must work with Texas Child Protective Services, and informed them she is able to restrict their parental rights or even terminate them.
The judge also ordered maternity and paternity testing of both mothers and fathers. A mobile unit will be used to collect DNA samples from the children on Monday, and from parents on Tuesday, Walther said.
FLDS women sat silent and motionless inside Walther's courtroom upon hearing the ruling. After the judge left the courtroom, many huddled with their attorneys and listened as the lawyers explained the meaning of the decision.
Inside the city hall auditorium one block away, many parents watching a video feed of the courtroom dropped their heads in sadness and walked out, one by one, following the ruling. Richard, an FLDS father of seven children in state custody who declined to provide his last name, said :"It's just a continuation of a bad thing."
Another FLDS father, who asked not to be identified, said: "I think every parent in America ought to go home and hug their kids in case CPS come into their homes and gets them and does this joke of a hearing to determine their status."
Prior to rendering the verdict, Walther described the difficulty of her task.
"This is the hardest, toughest decision a judge makes every day," she said. "It's no easy decision to rip families apart. There is no easy way to do this."
CPS spokeswoman Marleigh Meisner said her agency was pleased with the decision and felt the judge had taken into account evidence that was very important to the case, which she said was not about religion but about keeping children safe.
The agency will now begin to immediately find foster placements for the children. When asked whether those placements would be with relatives or foster families, Meisner said relatives would be only considered when appropriate.
Each child will have an individual hearing, and those proceedings must be finished by June 5. It's possible Walther will line up special masters and judges to help with the hearings.
One attorney representing two children, ages 8 and 9, left the city hall auditorium in tears. Deborah Cascino said she had mixed feelings about the judge's order.
"I just feel sorry for the parents, and I feel sorry for the children," said Cascino, who has been a family lawyer for four years and said she knows parents always want their children back.
Whether the judge made the right ruling, she said, only time will tell.
Prior to the ruling, several attorneys representing the mothers had requested that Walther allow the women and older boys to have their cell phones back to communicate with each other and their attorneys.
"The concern that we have is to make sure that we have access to our clients, and the opportunity to show their willingness and ability to keep their children safe," said D'Anne Johnson, an attorney with Rio Grande Legal Aid Society representing one of the mothers.
Walther did not rule on the request.
Shortly before the ruling, FLDS mothers testified they were willing to do whatever the judge required, including moving away from the sect's YFZ ranch and getting jobs, to regain custody of their children.
Earlier today, William John Walsh, a Mormon scholar who has studied the FLDS religion for 18 years, said it's not part of FLDS doctrine or scripture that teenage girls marry and have sex with older men.
Texas authorities earlier had said that one reason for the raid was to protect underage girls from arranged marriages with older men in the sect.
Texas Child Protective Services chief investigator Angie Voss testified yesterday boys in the polygamous sect are groomed to become perpetrators of sexual assault, and girls become their victims. Today, she rejected scenarios proposed by attorneys that might lead to the return of the children.
Psychiatrist Bruce Perry of Texas, also took the stand this morning. Perry has worked with children from the Branch Davidian sect and said although he has found much to be admired about the FLDS, "the environment is authoritarian."
Perry testified that "young girls who are 14, 15 or 16 are not emotionally mature enough to enter into healthy sexual relationships" and also focused his testimony on the limited choices available to FLDS children.
Friday was the second day of the historic custody hearing that brought together hundreds of volunteer attorneys representing the children, FLDS parents, and reporters.
Officials have said they do not know if the 16-year-old girl who prompted the raid is in state custody. Authorities say a girl named Sarah made a series of telephone calls to the crisis line at NewBridge Family Shelter on March 29 and March 30.
Court documents say the girl spoke of becoming the seventh wife of a 50-year-old man named "Dale" and conceiving her first child at 15. She described being beaten by her husband, once so badly she needed treatment at a hospital for broken ribs, and said she wanted to leave the ranch.