From the National Archives
The agencies listed below are repositories for Confederate pension records. The veteran was eligible to apply for a pension to the State in which he lived, even if he served in a unit from a different State. Generally, an applicant was eligible for a pension only if he was indigent or disabled. In your letter to the repository, state the Confederate veteran's name, his widow's name, the unit(s) in which he served, and the counties in which he and his widow lived after the Civil War. Some repositories also have records of Confederate Homes (for veterans, widows, etc.), muster rolls of State Confederate militia, and other records related to the war.
For information on procedures and fees for requesting copies of records, contact the appropriate repository.
For the list of agencies: Click Here.