Nichols said he also has evidence that between September 1989 and July 2006, Jeffs either performed or witnessed 67 other marriages to underage girls, and that he also performed or witnessed 500 other "bigamist" marriages.
Other alleged bad acts by Jeffs include six other acts of unlawful sex; breaking up 300 families by reassigning wives and children, and taking property; expelling young men from the FLDS to have more girls for himself and his inner circle; having "contempt for the law of man;" creating refuges to hide women from law enforcement; and evading law enforcement himself.
All are actions that for decades have subjected the FLDS to public criticism.
Other Utah polygamous groups applauded the Thursday's verdict and denounced Jeffs for committing sex crimes while hiding behind a "false pretense of a religious ideology."
Jeffs' older half-sister said she was pleased with the verdict.
"I'm happy that he's having to answer for his bad acts," said Elaine Jeffs, who left a plural marriage in 1984.
But Elaine Jeffs, standing on the steps of the Tom Green County Courthouse, said the conviction may not make a big difference to her brother's followers.
"They just make a martyr out of him," she said, "and the only way things are going to happen in the FLDS is it must come from within. People must change their minds; change their ideas."
The sentencing phase of Jeffs' trial continues today and could go into next week.
Jeffs showed no reaction as Walther read the verdict, which arrived after 3 1/2 hours of deliberation.
Earlier in the day, Jeffs who acted as his own attorney stood silent for nearly every moment of his allotted 30 minutes for a closing argument.
His only statement during closings was to mutter, "I am at peace."
Jeffs never cross-examined any prosecution witnesses, never directly challenged any prosecution evidence and called only a single witness on his own behalf. Throughout his defense, Jeffs never mentioned the sexual assault charges against him not even to proclaim his innocence.
He did make frequent objections, claiming his religious freedom was being violated and his faith persecuted, but none of them were sustained by the judge.
Jeffs' standby attorney, Deric Walpole, told reporters: "Any time there's a loss, we are disappointed." He declined to say whether the outcome could have been different if Jeffs had professional legal representation.
The conviction marks perhaps the lowest point yet for the Jeffs, who still claims thousands of followers in the FLDS, but has battled legal problems since 2004, when he refused to answer lawsuits filed against the trust he oversaw as the sect's president.
In 2007, a St. George jury convicted Jeffs of rape as accomplice for encouraging a 14-year-old girl to marry and have sex with her 19-year-old cousin and he was sentenced to up to life in prison. That conviction was overturned by the Utah Supreme Court based on faulty jury instructions, but Texas law professors have said that Texas appeals courts seldom overturn jury verdicts.
During the first phase of the Texas trial, Jeffs' only defense witness was FLDS member J.D. Roundy, who testified a total of five hours about FLDS beliefs and doctrine. Jeffs continued to ask theological questions of Roundy, despite repeated objections by the prosecution which the judge upheld that the questions were irrelevant to the sexual assault charges.
Walther finally had enough Thursday morning and excused Roundy from the witness stand. Then, when Jeffs went three minutes without calling another witness, Walther declared Jeffs had rested his defense case.
Prior to closing arguments, with the jury out of the room, Jeffs made a motion to allow the jury find him innocent based on "pure religious intent. Walther denied the motion.
During the prosecution's closing argument, Nichols stressed to jurors that the so-called religious persecution and freedom issues Jeffs had raised in his defense should have nothing to do with their deliberations.
"This case is not about any people," Nichols said. "This case is not about any religion. This case is about Warren Steed Jeffs and what he has done."
During his time for giving a closing argument, Jeffs spent the first 20 minutes standing at the defense table, staring forward with his hands folded at his waist. Then he turned his gaze to the prosecutors and jury. Four minutes after saying, "I am at peace," Jeffs sat and let his remaining time expire.
Walther had announced the passing of each five-minute increment. Members of the jury fidgeted in their chairs and sat with their arms folded.
In the gallery, pews could be heard squeaking. One person read a newspaper. Another read a magazine. One of Jeffs' standby attorneys surfed the Internet on his laptop.
When Jeffs' half-hour expired, Walther declared it was time to give the case to the jury.
The penalty phase of the trial commenced about an hour after the verdict was read.
During previous trial testimony, the jury heard an audio recording of Jeffs purportedly having sex with the 12-year-old girl he is accused of taking as a wife with two other wives present and possibly participating.
Jeffs is heard panting and breathing heavily throughout the 21-minute tape recording. And while it was difficult to hear some portions due to background noise, a girl's voice occasionally can be heard and Jeffs twice refers to the victim by name.
The girl is not heard resisting, and there are no overt references to sex.
But prosecutors had earlier presented testimony that certain phrases heard on the tape are used by Jeffs and his followers to refer to sex, including "heavenly comfort" and "heavenly sessions."
Just before the tape ends, Jeffs is heard saying, "In the name of Jesus Christ, Amen."
And three female voices are heard replying, "Amen."
Prosecutors say Jeffs "married" one of his victims when she was 14 years old. Jeffs got the girl pregnant when she was 15.
A DNA expert testified Monday there is a greater than 99.9 percent certainty that Jeffs is the father of the girl's baby.
Jeffs married the 12-year-old girl on July 27, 2006 at the FLDS's Yearning for Zion Ranch in Eldorado, Texas, according to records seized by police during a massive 2008 raid at remote ranch.
When Jeffs told the girl's father of the planned marriage, the father replied, "I am willing," and smiled, according to Jeffs' priesthood records. The father was present at the wedding ceremony.
Neither of the girls testified for the prosecution.
Marshall Doig contributed to this report.
The evidence against Warren Jeffs
Sexual assault of a child
Victim was a 15-year-old girl; assault occurred in 2005.
The girl had a child, and a DNA expert testified Jeffs is the baby's father with more than 99.9 percent certainty.
FLDS church records purportedly show her parents were present for her marriage at age 14.
Pictures of the girl pregnant and with the baby were seized in the 2008 raid on the FLDS ranch.
Three audio recordings were made involving the girl, including one of Jeffs instructing wives on group sex.
Aggravated sexual assault
Victim is a 12-year-old girl; assault occurred in 2006.
Prosecutors introduced several pictures of Jeffs kissing, cuddling the girl.
Jeffs also talks about the girl in his personal journals, or priesthood records.
The prosecution also presented FLDS records of the marriage seized in the raid.
Prosecution rested with audio recording of the assault.
Both victims were subpoenaed by prosecutors but did not appear.
The trial, thus far
Day 1 • Jury selection begins. Jeffs' attorney requests a trial delay, but is denied.
Day 2 • Jury selection was expected to last another day, but panel is chosen at the end of an 11-hour day.
Day 3 • Judge Barbara Walther denies a defense request to suppress evidence gathered in a massive 2008 raid on the FLDS Yearning for Zion Ranch, but agrees to hear arguments on the evidence from a Cadillac Escalade Jeffs was riding in during his 2006 arrest.
Day 4 • As court opens for the day, Warren Jeffs stands and delivers a halting 30-minute speech, saying he has fired his team of high-profile attorneys and wants to represent himself. But after Walther denies a request for more time, he spends the rest of the day silently staring straight ahead.
Day 5 • Jeffs breaks his silence, first with a nearly hourlong, sermon-like speech defending polygamy and saying the trial violates his freedom of religion, then with a so-called revelation from God threatening "sickness and death" to those involved in the prosecution.
Day 6 • A forensic DNA expert testifies that Jeffs is the father of a child born to the then-15-year-old girl with more than 99.9 percent certainty. Prosecutors introduce photos of Jeffs cuddling and kissing the 12-year-old girl. A defense motion to recuse Walther supported by two more written "revelations" is denied.
Day 7 • Prosecutors introduce three audio recordings, including one of Jeffs instructing the older victim and other wives about group sex. Jeffs objects every few minutes, talking in rambling sentences about the breaking of a "sacred trust."
Day 8 • The prosecution rests with yet another audiotape of the purported sexual assault on the 12-year-old girl. Jeffs launches his defense by calling one of his followers to the witness stand to read from Mormon Scripture and doctrine for nearly five hours.
Day 9 • Jeffs stood silently for 30 minutes during his closing statement, saying only, "I am at peace." Jury deliberates for about 3 1/2 hours before finding him guilty on both counts.
P The sentencing phase of Jeffs' trial continues Friday and possibly through next week. The same jury that convicted Jeffs will decide his punishment.