The Civil War Collection was assembled from multiple sources and is a collection of private papers and, to a limited extent, official records relating to the Civil War. It is arranged in six series. Series I. Union Records is divided into two subseries. Subseries A. Military and Official Documents contain enlistment rolls for Massachusetts, commissions, discharges, ration cards, passes and leaves of absence for soldiers, pension papers, documents issued by the Commonwealth of Massachusetts or the United States government, and a list of disloyal citizens of Alexandria, Virginia. Subseries B. Rolls of Enlisted Men consist of two roll books for men from Massachusetts, a list of men enrolled from Topsfield, Massachusetts, and a list of soldiers compiled after the war.

Series II. Confederate Records include documents regarding secession, documents and forms of the Confederate States of America; commissions, passes, medical records, regimental reports and rolls, requisition orders, and treasurer notes.

Series III. Naval Records is divided into two subseries. Subseries A. Ships' Papers is comprised of ships' official records from watch stations; instructions to pursers; order and letter books; and the personal notebook of Henry Test aboard U.S.S. Catskill. Subseries B. Correspondence and Personal Papers includes correspondence sent home from sailors; official correspondence between officers and the Navy Department; the diary of an unknown sailor aboard the U.S.S. Midnight; and testimonies regarding the rank restoration of Captain George Henry Preble following his dismissal from the Navy, after a Confederate ship, the CSS Florida, reached safe harbor in Mobile, Alabama during an 1862 blockade.

Series IV. Salem Clubs and Committees includes correspondence and financial records of the Army and Navy Union; Union Drill Club by-laws, list of members, meeting minutes, financial records, and circulars; correspondence and meeting minutes of the public safety committee; vouchers for money received by the Salem Citizens' Relief Committee; a list of subscribers to the National Five Cent Fund; lists of subscribers and financial records of the Salem Recruiting Committee; and documents relating to the Soldiers' and Sailors' Memorial Committee.

Series V. Collected Materials is divided into five subseries. Subseries A. Captured Confederate Documents is comprised of documents collected by Union soldiers, some of which were sent directly to Dr. Henry Wheatland, Secretary of the Essex Institute. The papers collected by William Lewis Welch include several North Carolina legal documents dating back to 1780; a portion of a plantation journal; papers related to the purchase of slaves; correspondence between soldiers and their families; and letters written by "the Secession Ladies". Subseries B. Correspondence includes the letters of Union soldiers and their families; these are mostly written by Essex County, Massachusetts families. Subseries C. Maps and Newspaper Clippings include maps collected from the New York Herald, Harper's Weekly, and the New York Semi-Weekly Tribune. A few articles and pictorial scenes printed in the same newspapers are also included in this subseries. A single hand-drawn map of Port Hudson during the 48 day siege of United States forces in 1863 can be found in this series. Subseries D. Ephemera and Currency is comprised of railroad tickets, shipping labels, a songbook, mitten patterns, commemorative ribbons, and a broadside advertising a 4th of July celebration at Fort Warren. There is also a folder of 12 bills of currency ranging from three cents to one-hundred dollars. The bills are from Pennsylvania and various Confederate States. Subseries E. Union Items include land grants to Massachusetts soldiers, a copy of the New Testament and a medal given to a Massachusetts Lieutenant, and a handwritten history of participation in the war by Captain Charles Manning of Salem.

Series VI. Photographs includes War Views, an album of Matthew Brady and Timothy H. Sullivan prints. A second album contains cabinet card portraits of officers and some foreign dignitaries, while two other volumes contain cartes de visite of officers. There are two cartes de visite of Frances Clalin Clayton, dressed in both a dress and her Union uniform. The loose photographs in this series are organized by subject matter and location. The series also includes photographic images of other visual materials representing scenes from the Civil War and leaves from the Photographic History of the Civil War.