In 1861 he was granted permission to recruit a regiment in Philadelphia, which was made up of mostly German emigrants. He played a key role in organizing the 75th Pennsylvania Volunteer Infantry, and he was named its Colonel and commander on September 30, 1861. He served in the division of Louis Blenker. In his report on the medical condition of the Army of the Potomac in February 1862, the army's chief surgeon and medical director, Charles Tripler, reported that just over 5 percent of Bohlen's brigade was listed as sick, which was on par with the other brigades in Blenker's division. The medical report gave Bohlen's strength as follows: 58th New York Infantry Regiment, 650; the 35th Pennsylvania Infantry Regiment, 732; and the 40th Pennsylvania Infantry Regiment, 868, for a total strength of 2,250.
Bohlen was appointed Brigadier General, U.S. Volunteers, on April 28, 1862. He commanded the 3rd Brigade of Carl Schurz's Division in the Valley Campaign against Stonewall Jackson in the spring of 1862. His brigade participated in the Battle of Cross Keys, 8 June 1862, but did not fight at the Battle of Cedar Mountain, 9 August 1862, as Sigel's division was encamped at Culpeper Court House at the time of the battle.
At the Battle of Cross Keys, Bohlen supported the brigade of Julius Stahel of Blenker's division. Bohlen formed his troops behind Stahel's just to the east of the Port Republic Road, southwest of the Evers house. Bohlen's brigade comprised the 54th New York Infantry Regiment on the left, the 58th New York Infantry Regiment, the 74th Pennsylvania Infantry Regiment, and, on the right, the 75th Pennsylvania Infantry Regiment. Battery I of the 1st New York Light Artillery Regiment occupied the center. Bohlen positioned this battery forward of his infantry. An artillery officer in Blenker's division moved this battery without Bohlen's permission. Bohlen moved it back again. When the artillery officer ordered the battery to move a half a mile to the rear, Bohlen belayed that order, but the battery moved anyway, "against my positive order to remain."
On 21 August, Confederate General Robert E. Lee marched his army north along the Rappahannock river. His objective was to cross the river beyond the enemy's right flank. Union General John Pope anticipated this move and defended the various fords to the north of Rappahannock Station. The afternoon of 22 August, Bohlen's corps commander, General Franz Sigel, sent Bohlen's infantry brigade across the river to reconnoiter the ground to the west of Freeman's Ford. Once across, Bohlen formed a skirmish line to go forward. It soon made contact with Confederate General Isaac Trimble's infantry brigade, hidden in heavy woods. Trimble attacked. Bohlen committed his entire brigade to the fight, but the enemy proved too strong. Bohlen gave the order to withdraw, and his men retreated back across the Rappahannock One of Bohlen's men admitted that the brigade retreated "so fast that we came near forgetting to stop."
In his official report, Confederate General Robert E Lee described the fight as "a short but spirited engagement," in which Bohlen's brigade sustained "heavy loss." Union General John Pope, the commander of the Army of Virginia, mentioned Bohlen's death briefly in his official report, dated 24 August 1862: "Our losses during the last three days have been quite heavy, among the killed being Brigadier-General Bohlen, commanding a brigade in Sigel's corps"
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