As tension mounted between the two groups, a number of skirmishes and battles occurred between the two factions, with the anti-slavery proponents referred to as Jayhawkers, and the pro-slavery advocates referred to as Bushwhackers or Border Ruffians.

The battles between the Jayhawkers and Bushwhackers continued even after Kansas was declared a “Free-State” and into the Civil War. By this time, the term was so well-known that many Confederates referred to any Kansas troops as Jayhawkers, but this was not the case. The true Jayhawkers were guerilla fighters that were often undisciplined, unprincipled, thieving and murderous. Because of their ruthless ways and tendency towards theft, the term “Jayhawking” became widely used as a synonym for stealing, and the term “Jayhawk” itself, was also used as an epithet for any marauder, robber, or thief.

Liking the tough image the term conveyed, Kansas soldiers continued to use the term and members of the Seventh Kansas regiment, commanded by Colonel Charles R. Jennison, were widely known as Jayhawkers. Jennison's troops, who wore red breeches, were also referred to as “Redlegs.” Other prominent Jayhawkers of the time were renowned politician, James H. Lane who commanded what was known as "Lane's Brigade," and Daniel R. Anthony, an ardent abolitionist and the brother of suffragette Susan B. Anthony. In many cases, true Jayhawkers and Redlegs refused to join units officially sanctioned by the U.S. Army; however, guerrillas on both sides of the Missouri-Kansas border achieved some measure of legitimacy through sanction from the Federal and Confederate governments.

During the Civil War, Jayhawker bands invaded Missouri, often committing some of the  most notorious atrocities of the conflict including the Sacking of Osceola on September 23, 1861, led by James H. Lane, in which the entire town was set aflame and at least nine male residents were killed.

Two years later, when William Quantrill attacked Lawrence, Kansas in August, 1863 in what has become known as the Lawrence Massacre, Confederate guerillas could be heard shouting, "Remember Osceola!" Though Lane was in residence in Lawrence at the time, he was able to escape the attack by racing through a cornfield in his nightshirt.