Accompanied by sheriff's deputies, he arrived at the Purgatory Correctional Facility in Hurricane shortly after noon, said Washington County Sheriff's Lt. Rob Tersigni.
An initial court appearance was expected Wednesday before 5th District Judge James L. Shumate, though the court typically conducts initial appearances via video link from the jail. A public defender could be appointed for Jeffs then if he has no attorney.
Jeffs, 50, had been on the FBI's Ten Most Wanted list until his arrest last month during a chance traffic stop near Las Vegas.
Even behind bars, he is considered the leader of the Fundamentalist Church of Jesus Christ of Latter Day Saints, a polygamist sect with an estimated 10,000 followers, many in the twin towns of Hildale, Utah, and Colorado City, Ariz. The sect broke away from the Mormon church more than a century ago and has been disavowed by the Mormons.
Jeffs is charged in Utah with two felony counts of rape as an accomplice, accused of having arranged a "spiritual marriage" between a teenage girl and an older man. Each count carries a penalty of up to life in prison if convicted.
The alleged marriage took place some time within the past four years, when the girl was between age of 14 and 18, according to Washington County Attorney Brock Belnap. "Jane Doe," as the girl is referred to in court documents, objected to the marriage but was told by Jeffs that she must she must give herself "mind, body and soul" to her husband, court papers said.
Jeffs, who decides which of his followers marry and to whom, told the girl that she would lose her salvation if she did not obey her husband, court papers said.
It was not immediately clear Tuesday if Jeffs has hired an attorney.
Jail records released Tuesday by Las Vegas police show Jeffs was visited during his weeklong stay at the Clark County jail by two of his brothers, an investigator from Arizona and a lawyer from Las Vegas, Richard Wright, who met with Jeffs four times and also met at least twice with one of his brothers.
Wright, a defense lawyer, recently represented a politician charged with corruption and boxer Floyd Mayweather Jr., who was acquitted last year on charges stemming from a fight with a former girlfriend.
At Purgatory Correctional Facility, a 500-bed county jail 30 miles west of Hildale, Jeffs will be held in a small cell alone for 23 hours a day, with one hour for showers, exercise and phone calls, according to Sheriff Kirk Smith. He will be allowed up to two hours of visitation weekly.
Jeffs also faces felony charges in Arizona, accused there of arranging a marriage between a 16-old-girl and a 28-year-old man, who was already married.
As with the Washington County charges, the Mohave County, Ariz., counts — conspiracy to commit sexual conduct with a minor and sexual conduct with a minor, which each carry a penalty of two years in prison — do not accuse Jeffs of having sex with either girl, but that he encouraged others to do so.
By some estimates, Jeffs has more than 40 wives and about six dozen children who have lived in million-dollar homes that cover an entire Hildale city block, surrounded by 14-foot brick walls and locked gates. It's not known if his families remained on the premises while he was a fugitive.