Wood commanded a brigade in the Tennessee and Mississippi campaigns at the beginning of the war. He commanded a division in the Army of the Ohio, then in the Army of the Cumberland. Wood was present at the second day of the Battle of Shiloh. Wood was wounded during the Battle of Murfreesboro in December 1862. He suffered controversy at the Battle of Chickamauga, where he was blamed for contributing to William S. Rosecrans's defeat. On September 20, 1863, a breakdown in situational awareness by Rosecrans and poor staff work resulted in Wood receiving a seemingly senseless order that, if literally obeyed, required him to pull his division out of the line to the support of another division further to his left, dangerously creating an unprotected gap in the right of the line. Instead of verifying his commander's actual intent, Wood elected to regard the order as imperative and moved his division out of its position.