Meanwhile, the United States had acquired Utah from Mexico in 1848, as a result of the Mexican War. In 1849 the Mormons petitioned the U.S. Congress to admit their region, which they called the State of Deseret, to the Union. Congress denied the petition, but organized Utah Territory in 1850, with Young as governor and Fillmore as the capital. (Salt Lake City became the capital in 1856.) The territory encompassed Utah, most of Nevada, and parts of Wyoming and Colorado. (Land cessions in the 1860's reduced Utah to the size it is today.)

During the 1850's, thousands of additional Mormon settlers arrived in Utah, large numbers of them coming from Great Britain and Scandinavia. By mid-decade, the population was nearly 40,000. Although the Mormons had sought peaceful relations with Indian tribes in the area, the expansion of settlement led to clashes. Wars were fought, 1853–54, and 1865–68. After the latter conflict, many of the Indians were removed to reservations.

From the earliest days of the territory, relations with the federal government had been strained by the Mormons' determination to run Utah free from federal control. Problems also arose over the practice of polygamy. (Mormon law allowed men to have several wives.) In 1857 President James Buchanan appointed non-Mormons to the governorship and to other territorial offices. The Mormons protested this action, and Buchanan dispatched federal troops to Utah to support his appointees. Young mobilized the Nauvoo Legion, the Mormon militia. Militia companies burned Army supply trains, but before the two armies could confront one another in full-scale battle, the "Utah War" was settled by compromise. However, antagonism between Mormons and the federal government continued for decades.

The only bloodshed that occurred during the war was the Mountain Meadows Massacre, in which an Indian party that included a few Mormons killed 120 members of a wagon train passing through Utah.

Utah underwent significant development beginning in the late 1860's. On May 10, 1869, the Union Pacific Railroad from the east and the Central Pacific Railroad from the west joined their tracks at Promontory, Utah, marking completion of the first transcontinental railway. ( The coming of the railroad gave the Mormons new markets for their crops and made it economically feasible for them to begin exploiting Utah's mineral resources. The railroad, however, also ended the Mormons' long isolation. By 1880 Utah's population had risen to 144,000, almost double that of 1869, and included more than 20,000 non-Mormons.

Opposition to Mormon economic and political domination of the territory and to the practice of polygamy had risen steadily in the 1870's and 1880's in other parts of the country and among non-Mormons in Utah. The federal government also was increasingly concerned about the Mormons' continuing resistance to outside authority, which it viewed as disloyalty to the United States. As a result, repeated petitions for Utah statehood (1856, 1862, 1882, and 1887) were denied. In 1887 the Edmonds-Tucker Act, depriving Mormons of their civil rights and confiscating Mormon church property, was passed.

In 1890 the Mormon church declared that it would no longer sanction polygamy. Civil rights were then restored and confiscated property returned to the church. In 1895 a constitution was written and ratified. It prohibited polygamy and gave women the right to vote. Statehood was finally granted on January 4, 1896, and Utah entered the Union as the 45th state.