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Different tribes of paleo-Indians lived in Illinois as long ago as 8000 BC. By 2000 BC, the cultivation of plants and use of ceramics were known to village dwellers; the first pottery appeared during the Woodland phase, a millennium later. Between 500 BC and AD 500, skilled Hopewellian craftsmen practiced a limited agriculture, developed an elaborate social structure, and constructed burial mounds. Huge mounds, which still exist, were built along the major rivers by the Middle Mississippian culture, about AD 900.

It is not known why the early native civilizations died out, but by the time white explorers arrived in the 17th century, the state was inhabited by seminomadic Algonkian-speaking tribes. The Kickapoo, Sauk, and Fox lived in the north, while the shores of Lake Michigan were populated by the Potawatomi, Ottawa, and Ojibwa. The Kaskaskia, Illinois (Iliniwek), and Peoria tribes roamed across the central prairies, and the Cahokia and Tamoroa lived in the south. Constant warfare with tribes from neighboring areas, plus disease and alcohol introduced by white fur traders and settlers, combined to decimate the Native American population. Warfare with the whites led to a series of treaties, the last in 1832, that removed all of the Indians to lands across the Mississippi.

French missionaries and fur traders from Quebec explored the rivers of Illinois in the late 17th century. Father Jacques Marquette and trader Louis Jolliet were the first to reach the area now known as the state of Illinois in 1673, when they descended the Mississippi as far as the Arkansas River and then returned by way of the Illinois River. The first permanent settlement was a mission built by French priests at Cahokia, near present-day St. Louis, in 1699. It was followed by more southerly settlements at Kaskaskia in 1703 and Ft. Chartres in 1719. In 1765, pursuant to the Treaty of Paris (1763) that ended the French and Indian War, the British took control of the Illinois country, but they established no settlements of their own. Most of the French settlers were Loyalists during the American Revolution. However, they put up no resistance when Virginia troops, led by George Rogers Clark, captured the small British forts at Cahokia and Kaskaskia in 1778. Virginia governed its new territory in desultory fashion, and most of the French villagers fled to Missouri. In 1784, Virginia relinquished its claim to Illinois, which three years later became part of the newly organized Northwest Territory. In 1800, Illinois was included in the Indiana Territory. Nine years later the Illinois Territory, including the present state of Wisconsin, was created; Kaskaskia became the territorial capital, and Ninian Edwards was appointed territorial governor by President James Madison. A territorial legislature was formed in 1812. During the War of 1812, British and Indian forces combined in a last attempt to push back American expansion into the Illinois country, and much fighting took place in the area. On 3 December 1818, Illinois was formally admitted to the Union as the 21st state. The capital was moved to Vandalia in 1820 and to Springfield in 1839.

Apart from a few thousand nomadic Indians and the remaining French settlers and their slaves, Illinois was largely uninhabited before 1815; two years after statehood, the population barely exceeded 55,000. The withdrawal of British influence after the War of 1812 and the final defeat of the Indian tribes in the Black Hawk War of 1832 opened the fertile prairies to settlers from the south, especially Kentucky. The federal government owned most of the land, and its land offices did a fast business on easy terms. Before the 1830s, most of the pioneers were concerned with acquiring land titles and pursuing subsistence agriculture, supplemented by hunting and fishing. An effort in 1824 to call a constitutional convention to legalize slavery failed because of a widespread fear that rich slaveholders would seize the best land, squeezing out the poor yeoman farmers. Ambitious efforts in the 1830s to promote rapid economic development led to fiscal disaster. Three state banks failed; a lavish program of building roads, canals, and railroads totally collapsed, leaving a heavy state debt that was not paid off until 1880. Despite these setbacks, the steady influx of land-hungry poor people and the arrival after 1840 of energetic Yankee entrepreneurs, all attracted by the rich soil and excellent water routes, guaranteed rapid growth.

Although Illinois gradually eliminated French slavery and even served as a conduit to Canada for slaves escaping from the South, the state was deeply divided over the slavery issue and remained unfriendly territory for blacks and their defenders. The abolitionist leader Elijah P. Lovejoy was killed in Alton in 1837, and as late as 1853 the state passed legislation providing that free blacks entering Illinois could be sold into slavery. In 1856, however, the new Republican Party nominated and Illinois voters elected a governor, William H. Bissell, on a reform program that included support for school construction, commercial and industrial expansion, and abolition of slavery. During the Civil War, Illinois sent half its young men to the battlefield and supplied the Union armies with huge amounts of food, feed, and horses. The strong-handed wartime administration of Republican Governor Richard Yates guaranteed full support for the policies of Abraham Lincoln, who had been prominent in Illinois political life since the 1840s and had been nominated for the presidency in 1860 at a Republican convention held in Chicago. Democratic dissenters were suppressed, sometimes by force, leaving a legacy of bitter feuds that troubled the "Egypt" section (the southern third of the state) for decades thereafter.

Economic and population growth quickened after 1865, as exemplified by the phenomenal rise of Chicago to become the principal city of the Midwest. Responding to opportunities presented by the coming of the railroads, boosters in hundreds of small towns and cities built banks, grain elevators, retail shops, small factories, ornate courthouses, and plain schools, in an abundance of civic pride. The Democrats sought the support of the working class and small farmers, assuming an attitude of hostility toward banks, high railroad freight rates, protective tariffs, and antiunion employers, but they failed to impose any significant restraints on business expansion. They were more successful, however, in opposing prohibition and other "paternalistic" methods of social control demanded by reformers such as Frances Willard, a leader in the Women's Christian Temperance Union, and the Prohibition Party. In Chicago and other cities the Democrats were less concerned with social reform than with building lucrative political machines on the backs of the poor Irish, Polish, and Czech Catholic immigrants, who kept arriving in large numbers. Statewide, Illinois retained a highly competitive two-party system, even as the excitement and high voter turnouts characteristic of 19th-century elections faded rapidly in the early 20th century.

During the second half of the 19th century, Illinois was a center of the American labor movement. Workers joined the Knights of Labor in the 1870s and 1880s and fought for child-labor laws and the eight-hour day. Union organizing led to several spectacular incidents, including the Haymarket riot in 1886 and the violent Pullman strike in 1894, suppressed by federal troops at the behest of President Grover Cleveland. A coalition of Germans, labor, and small farmers elected John Peter Altgeld to the governorship in 1892. After 1900, Illinois became a center of the Progressive movement, led by Jane Addams and Republican Governor Frank Lowden. Lowden reorganized the state government in 1917 by placing experts in powerful positions in state and municipal administrations.

After the great fire of 1871 destroyed Chicago's downtown section (but not its main residential or industrial areas), the city's wealthy elite dedicated itself to rebuilding Chicago and making it one of the great metropolises of the world. Immense steel mills, meat-packing plants, and factories sprang up, and growth was spectacular in the merchandising, banking, and transportation fields. Their fortunes made, Chicago's business leaders began building cultural institutions in the 1890s that were designed to rival the best in the world: the Chicago Symphony, the Art Institute, and the Field Museum of Natural History. The World's Columbian Exposition of 1893 was a significant international exhibition of the nation's technological achievements, and it focused worldwide attention on what was by then the 2nd-largest American city. A literary renaissance, stimulated by the new realism that characterized Chicago's newspapers, flourished for a decade or two before World War I, but the city was recognized chiefly for its contributions in science, architecture, and (in the 1920s) jazz.

The first three decades of the 20th century witnessed almost unbroken prosperity in all sections except Egypt, the downstate region where poor soil and the decline of the coal industry produced widespread poverty. The slums of Chicago were poor, too, because most of the hundreds of thousands of new immigrants arrived virtually penniless. After 1920, however, large-scale immigration ended, and the immigrants' steady upward mobility, based on savings and education, became apparent. During the prohibition era, a vast organized crime empire rose to prominence, giving Chicago and Joliet a reputation for gangsterism, violence, and corruption; the most notorious gangster was Al Capone. Money, whether legally or illegally acquired, mesmerized Illinois in the 1920s as never before—and never since.

The Great Depression of the 1930s affected the state unevenly, with agriculture hit first and recovering first. Industries began shutting down in 1930 and did not fully recover until massive military contracts during World War II restored full prosperity. The very fact of massive depression brought discredit to the pro-business Republican regime that had run the state with few exceptions since 1856. Blacks, white ethnics, factory workers, and the undereducated, all of whom suffered heavily during the early years of the Depression, responded enthusiastically to Franklin Roosevelt's New Deal. They elected Henry Horner, a Democrat, to the governorship in 1932, reelected him in 1936, and flocked to the new industrial unions of the Congress of Industrial Organizations, founded in 1938.

World War II and its aftermath brought prosperity, as well as new anxiety about national security in a nuclear age. The chilling events of the 1960s and 1970s—assassinations, the Vietnam war, the race riots, and the violence that accompanied the 1968 Democratic National Convention in Chicago—helped reshape many people's attitudes in Illinois. The problems attendant on heavy industrialization, particularly air and water pollution and urban decay, began to be addressed for the first time. This transformation was perhaps best exemplified in Chicago, where voters elected Jane Byrne the city's first woman mayor in 1979 and chose Harold Washington as its first black mayor in 1983.

The economy of Illinois, like those of other Rust Belt states, suffered a severe recession in the early 1980s. By the end of the decade, the economy had begun to rebound, but many industrial jobs were permanently lost, as industries sought to improve efficiency and productivity through automation. In 1990, the unemployment rate in Illinois was 7.2%, in contrast to the national average of 5.2%. Into the 1990s, industrial losses slowed while the service industries and the newer high-tech industries, which had gained a foothold in the greater Chicago area, became more dominant. By 1998, as the US experienced the longest sustained economic boom in its history, many in Illinois felt the prosperity. The state ranked 8th highest in the nation for per capita income and by 1999 Illinois' unemployment rate was 4.3%, in line with the national average. The poverty rate also fell during the decade, from 11.9% in 1989 to 10.1% a decade later.

Chicago's infrastructure has suffered several problems in recent years. In 1992 there was a rupture in the 60-mi (96-km) maze of tunnels that lies beneath downtown. Water from the Chicago River flooded basements and sub-basements in the city's central Loop district with as much as 30 feet of water, forcing the temporary closure of many downtown buildings and businesses, including the Chicago Board of Trade, City Hall, and Marshall Fields department store. In mid-August 1999 the downtown area was without power when a substation failed. About 2,300 Commonwealth Edison customers in the Loop, including skyscrapers, numerous businesses, and university buildings, were without electricity. Again buildings were forced to close, sending thousands of workers home early. Later that month ComEd suffered another high-profile outage when power was lost at the city's popular Field Museum, forcing its closure. In 2000 barge and other commercial boat operators on the Chicago River complained that the increase in recreational boater traffic on the waterway posed a serious danger to safety.

In June 2000 a panel of experts convening for a legislative history roundtable in Springfield concluded that the state's 1980 cutback amendment, which reduced the size of the Illinois General Assembly by one-third, had been a detriment to state government for two decades. The 1980 amendment ended Illinois' system of three-member house districts; experts argued that the old system had encouraged Republicans and Democrats to work together and that the new, one-member house district system resulted in "a higher degree of partisanship and bitterness."

Meanwhile, the state was embroiled in a bribe-for-licenses scandal involving Governor George Ryan. It was alleged that truck-driver licenses were issued in exchange for campaign contributions (from trucking companies) when Ryan was secretary of state. Indictments had been handed down to some state officials, but the governor insisted he knew nothing about the contributions and said if the accusations proved to be true, the money would be contributed to charities. Ryan left after one term in office due to the scandal, to be succeeded by Rod Blagojevich.

In 2003, the state had a $5 billion budget deficit, and was experiencing the worst recession in two decades. In 2002, Illinois lost 23,000 manufacturing jobs. In his State of the State Address, Governor Blagojevich targeted four areas in need of attention: jobs, schools, health care, and crime. In June 2003, the Illinois legislature passed a $10 billion budget allowing for increased school spending. The budget also called for increasing casino taxes and eliminating tax exemptions for trucking, chemical, insurance, and other industries.