Officials hope the samples, to be taken by cheek swabs from the children and their parents, will help sort out the confusing family relationships in a convoluted custody case that has strained the resources of the child welfare system and the courts.
The testing is being conducted in the San Angelo Coliseum, where most of the children have been held since last week.
Judge Barbara Walther ordered the tests at the request of state officials, who have complained that members of the Fundamentalist Church of Jesus Christ of Latter Day Saints have continually changed their names, possibly lied about their ages and sometimes had difficulty naming their relatives.
The process will likely take about half an hour per sample because of the paperwork and care needed to avoid contamination, said Darrell Azar, a spokesman for Child Protective Services. The tests could take three or four days to be completed.
A certain number of DNA markers - segments of the DNA with specific genetic characteristics - are tested to determine whether two people are related. If any uncertainties arise, analysts test additional markers.
Three male members of the sect said in an interview aired on CBS's "Early Show" Monday that they would cooperate in DNA testing if it would help them get the children back.
"Whatever we need to do to get them back in their peaceful homes," a man identified only as Rulan said.
Meanwhile, many of the men in the polygamist sect told Early Show co-anchor Maggie Rodriguez that they.
State prosecutors have argued that the FLDS church encourages underage marriages and births, subjecting children to sexual abuse or the imminent risk of abuse. "Rulan" said sect members are reconsidering whether girls under 18 should have sex with adult men.
"Many of us perhaps were not even aware of such a law," he said. "And we do reconsider, yes. We teach our children to abide the law."
When the DNA sampling is completed, state officials will begin to relocate some of the 416 children staying at the coliseum and will separate the children younger than 4 years from adult mothers.
Officials say family relationships in the sect can be confusing to outsiders because the children of more than one wife live in the same household.
The children identify all the women in the house as their mothers, and if a father leaves the community, children and mothers are reassigned to another man, a child welfare investigator testified during a hearing last week.
Mothers of the youngest children had been allowed to stay with the children before the judge's order on Friday. But that arrangement will end after they are moved from the coliseum, Azar said.
He said it's not clear how soon the children will be moved, but state workers will try to keep them grouped together with siblings or others from the community.
They'll also try to shield the children, raised in an insular community with no television and little contact with outsiders, from overexposure to mainstream society.
"We're going to try to keep the children in groups so I don't think we're talking about your traditional foster setting," Azar said.
After two days of testimony, Walther ordered that all the children swept up in the raid of the Eldorado compound remain in state custody.
The custody case is one of the nation's largest and most complicated. The ruling Friday capped two days of testimony that sometimes became disorderly as hundreds of lawyers for children and parents competed to defend their clients in two rooms linked by a video feed.
The children, including 130 children younger than 4 years and two dozen adolescent boys, will receive individual hearings before June 5.
Law enforcement officers raided the Yearning For Zion Ranch on April 3. The raid was prompted by calls made to a family violence shelter, purportedly by a 16-year-old girl who said her 50-year-old husband beat and raped her. That girl has never been identified.