In 1861, Sigel was commissioned Colonel of the 3rd Missouri Infantry. However, following his leadership at Carthage, Missouri, he was promoted to the rank of brigadier general. Sigel commanded a brigade in the Army of Southwest Missouri from January to February 1862. He was involved in the battles at Wilson's Creek. and Pea Ridge. In March 1862, he was appointed a major general. Three months later, he fought against Stonewall Jackson in Shenandoah Valley. In the Second Battle of Manassas, he served to command a wing of the Union army, however, it was a Confederate victory. In the winter of 1863, his health forced Sigel to rest from active duty. He returned in March 1864, but he was defeated at New Market. In July, he commanded the Union forces at Harpers Ferry , but he was soon relieved of his command for "lack of aggression".