The Loyalty and Security subseries (24.36 linear feet) documents the ACLU's monitoring of and fight against due process abuses that resulted from perceived national security threats during the Cold War. It is arranged chronologically by year and then divided by the headings: miscellaneous, cases, Congressional investigating committees (excluding HUAC), Federal Loyalty Program, Fifth Amendment, House Committee on Un-American Activities (HUAC), legislation, military security, private industry, and sedition and subversion. The files contain correspondence, memoranda, manuscripts, reports, legal documents, and printed materials.

Cases is the largest heading within the subseries and documents individual's cases in which the ACLU had an interest. The cases are organized by subjects including civilian loyalty, Coast Guard loyalty, Fifth Amendment, government, Gwinn Amendment, general loyalty, contempt, military loyalty, private industry, sedition, Smith Act, and treason.

The Federal Loyalty Program files document President Truman's executive order of March 21, 1947, allowing the government to deny employment to anyone when "reasonable grounds exist for belief that the person involved is disloyal to the government of the United States." These files span the years 1947 through 1962. The Fifth Amendment files document when people refused to testify against themselves or others and the Gwinn Amendment files cover the issue of required loyalty oaths from individuals residing in public housing.

The HUAC files are extensive and document the activities of the committee in detail and the ACLU's efforts to curb their power. In addition to the subseries, there are several boxes devoted solely to HUAC and one box to "Operation Abolition," a propaganda film made by HUAC. "Operation Abolition" created much controversy due to the blatant distortion of the events surrounding a student protest against HUAC hearings in San Francisco. These files are located at the end of the Loyalty Security subseries. (Series 6, Audio-visual material includes a copy of "Operation Abolition.")

Much of the Legislative heading concerns efforts to prevent the passage of loyalty oaths in various states. The private industry heading primarily deals with questions of loyalty and loyalty oaths for defense industry workers. The Sedition and Subversion heading is comprised of materials concerning the Communist Party and other political groups or individuals suspected of wanting to overthrow the U.S. government.

Also included are two small headings. The files for 1952 contain research materials collected for the publication of the Judges and the Judged, a detailed report on blacklisting prepared by Merle Miller for the ACLU. In the 1953 run, ten files document the trial of Ethel and Julius Rosenberg for espionage and the ACLU response.

Related records include the Marshall Civil Liberties Trust Fund Records, the Elizabeth Gurley Flynn Ouster files, and the Mass Communications Subject Files (for materials on blacklisting) subseries.