Tilghman was commissioned colonel of the 3rd Kentucky Infantry on July 5, 1861, shortly after the start of the American Civil War. He was promoted to brigadier general in the Confederate States Army on October 18. When General Albert Sidney Johnston was looking for an officer to create defensive positions on the vulnerable Tennessee and Cumberland Rivers, he was unaware of Tilghman's presence in his department and another officer was selected. However, the Richmond government pointed out Tilghman's engineering background and he was finally chosen for the task. The original sites for Forts Henry and Donelson were selected by another general, Daniel S. Donelson, but Tilghman was then placed in command and ordered to construct them. The geographic placement of Fort Henry was extremely poor, sited on a floodplain of the Tennessee River, but Tilghman did not object to its location until it was too late. (Afterward, he wrote bitterly in his report that Fort Henry was in a "wretched military position ... The history of military engineering records no parallel to this case.") He also was desultory in managing its needed construction and that of the small Fort Heiman, located on the Kentucky bank of the Tennessee, and quarreled with the engineers assigned to the task. He did manage to do a more creditable job on the construction of Fort Donelson, which was sited on dry ground, commanding the river.