In Missouri at the beginning of the Civil War, volunteer Unionist Home Guard regiments were formed with the blessing of Federal authorities to oppose secessionist Governor Claiborne Jackson's secessionist dominated militia and his intent to deny Missouri enlistments into Federal service. Brigadier General Nathaniel Lyon was given authority by the War Department to organize the Home Guard on June 11, 1861.
By late 1861 most of the Home Guard regiments had been disbanded. They were replaced by a smaller Six-month militia under state rather than Federal control. This force was too expensive for the cash-strapped provisional government to maintain. It was also too small to be effective. In all five regiments, eleven battalions, and ten companies were formed as six-month militia. (Although the financial burden for this organization during the war was paid by Missouri, the state was finally reimbursed following the United States Congress April 17, 1866 passage of "An act to reimburse the State of Missouri for moneys expended for the United States in enrolling, equipping, and provisioning militia forces to aid in suppressing the rebellion.
The new Missouri State Militia (MSM) was primarily a mounted force active throughout the remainder of the war. Cavalry were necessary to pursue and confront fast moving mounted guerrillas, recruiters, and raiders. By April 1862 the Missouri State Militia consisted of fourteen cavalry regiments, three cavalry battalions, two light artillery batteries, an infantry regiment and several independent companies of various types. On February 13, 1862 however, the United States Congress limited the size of the force to 10,000 in an effort to control expenses. The exigencies of war produced delay by the Federal War Department in complying with this law--primarily through attrition. Eventually the militia would be reorganized into nine regiments of cavalry and one of infantry. This was accomplished through General Order Number 5 by the Missouri Adjutant General which broke up the 3rd, 5th, and 12th Missouri State Militia Cavalry regiments and distributed them among other regiments. The 2nd Battalion Missouri State Militia was also disbanded and the 11th regiment and 1st battalion had been consolidated within the 2nd Missouri State Militia Cavalry earlier.
An unusual aspect of the militia cavalry compared to conventional cavalry was the frequent integration of light artillery into regimental or battalion level actions. The additional firepower was often effective against guerrillas or raiders with no artillery of their own.
There was considerable controversy and intrigue surrounding the actions and officers of men of the Missouri State Militia Cavalry. Several officers were at times charged with inefficiency or worse during operations, particularly during Sterling Price's 1864 Raid. General Alfred Pleasonton relieved General Egbert Brown and John McNeil for "failure to obey an order to attack." Also relieved by Pleasonton in the same action was Colonel James McFerran of the 1st Missouri State Militia Cavalry "whose regiment was straggling all over the country, and he was neglecting to prevent it." Colonel Henry S. Lipscomb of the 11th Missouri State Militia Cavalry was relieved for not pursuing Joseph C. Porter more vigorously during the summer of 1862 and the regiment was consolidated with the 2nd.
With Confederate General Sterling Price openly supporting guerrilla activity in Missouri, on March 13, 1862, the Union head of the Department of the Missouri, Henry Halleck, issued orders stating that such activity was "contrary to the laws of war" and directing that such combatants "will be hung as robbers and murderers. The following month, Confederate President Jefferson Davis legitimized guerrilla warfare by authorizing bands of "partisan rangers" to be formed to operate behind Federal lines. As the primary force to confront such activity in Missouri, the Missouri State Militia hierarchy shortly afterwards issued a controversial order declaring the partisans to be "robbers and assassins" and directing that they "be shot down on the spot. The order further offered the partisans an out, stating that they would be spared should they surrender to Federal authorities and take an oath of allegiance and be placed on parole. Some militia commanders were afterwards accused of atrocities in carrying out the counter-guerrilla tactics, including conducting drum-head court martials, or sometimes not court martial at all then executing suspected guerrillas or Southerners who had violated their paroles. There were also several examples of execution of prisoners in retaliation for the deaths of Union/militia soldiers or citizens. (See the Palmyra Massacre for a notorious example.)
In contrast to these controversies, Governor Hamilton R. Gamble, praised the Missouri State Militia as "very efficient." In speaking of the Missouri State Militia, General John M. Schofield claimed that "these troops will compare favorably with any volunteer troops I have seen," specifically complimenting the Missouri State Militia in regard to drill, discipline and efficiency. Schofield subsequently became General-in-Chief of the United States Army after the war.
Militia cavalry units participated in most of the significant engagements in the state of Missouri from 1862 to 1864. They were eligible for re-enlistment and, unsually for militia, were eligible for Federal pensions.