Series I, Biographical and Memorabilia (1975-1987) includes, in addition to Agee's typewriter (which was bugged by the CIA, and for which permisssion is required to view), includes the certificate of his marriage to Gysele Ingool, biographical profiles, business cards, certificates, clippings, itineraries and travel request forms, two plaques, and other memorabilia.

Series II, Correspondence (1954-2006) is organized into three subseries: the alphabetical correspondence includes correspondence with his attorney and writing collaborator Melvin Wulf, various periodicals and publishers, including Lyle Stuart, Maurice Bishop (Prime Minister of Grenada (1979-83), the Social Democratic Party of Germany and its youth organization, Noam Chomsky and various progressive activists and authors around the world; the chronological correspondence subseries contain single or at most a few letters from diverse individuals of lesser reknown, ; and the foreign languages subseries contains correspondence, in German and to a lesser degree, Spanish, and concerns Agee's literary and political activities and connections. Note that Melvin Wulf also sometimes appears as a correspondent or author in series IV, Government Documents, and V, Legal Cases and Documents.

Series III, Datebooks (1975-2007) contains bound volumes containing both appointments and notes, some detailed. The datebooks combine features of ddate/appointment books with those of diaries and notebooks. Included is contextual information and notes about appointments, research notes and political ccommentary, sometimes commingled.

Series IV, Government Documents (1950-1989), contains materials obtained under the Freedom of Information Act, the largest number from the CIA, but also including documents from the Department of State (individual files on countries around the world, including several on Great Britain), the Department of Justice, and the FBI, and several small files from other agencies. The CIA files and Department of Justice files include, in addition to files requested by Agee about various activities of these agencies, also include files about Agee, and about the contested nature of the FOIA process. The FBI files are principally lists of deleted materials, i.e., materials not released, but there is also a list of released documents and well as some documents themselves.

Series V, Legal Cases and Documents, documents five lawsuits in which Agee was the plaintiff, and also contains a selection of legal documents from and correspondence with Agee's attornerys regarding other cases that were of interest to Agee. The majority of the series consists of affadavits and other legal documents from Agee's suit v. the United States Central Intelligence Agency, Federal Bureau of Investigation, National Security Agency, Department of State, and Department of Justice, seeking to obtain government documents under the Freedom of Information Act. There are a small number of files, chiefly legal correspondence, but with some legal documents, from two lawsuits in which Agee sought damages for allegedly being falsely accused of being responsible for the 1975 death of Athens, Greece CIA Station Chief Richard Welch. In this regard, Agee separately sued former First Lady Barbara Bush, charging that her Barbara Bush: A Memoir (1994) falsely made this claim. Agee also sued author George Crile, et al, on the same grounds re his book Charlie Wilson's War (Grove/Atlantic, 2003). Bush agreed to alter one paragraph in her book as per a 1997 settlement. For the Crile case a similar settlement was reached in 2004. From Agee's unsuccessful attempt to regain his passport by suing the Department of State are several files of clippings, correspondence, and legal documents. There is also one file of plaintiff's affadavits from the case Philip Agee v. United States of America: Civil Action No. 94-2020-WBB, To Recover Damages for Illegal and Tortious Acts Committed against the Plaintiff by the CIA.

Series VI, Subject Files (1950-2006) contains research files on countries, compiled by Agee, with a concentration on Latin America, and in paraticular Cuba and Nicaragua; files on individuals, organizations and topics, in particular sets of files on Aldrich Hazen Ames (1941- , a former CIA counter-intelligence officer and analyst, who, in 1994, was convicted of spying for the Soviet Union and Russia, which included revealing the names of CIA agents), and on Project Democracy, a Reagan-era foreign policy initiative; and files, including some legal documents on Agee's unsuccessful struggles against his expulsion, respectively, from Great Britain and the Netherlands. This series contains a broad range of printed ephemera, clippings files, speeches, internal documents of various organizations, and some letters.

Series VII, University Lectures, Teaching and Research Files (1948-1999) contains lectures and resarch materials for his talks and courses in both paper and electronic format. Topics include U.S. foreign intelligence activity, the extreme right in Europe, including the activities of former Nazis in Germany, and files on a course "Reinhard Gehlen (a Nazi who collaborated with U.S. intelligence agencies) and the Continuation of the German War against the USSR." Agee taught most frequently in Europe, and within Europe, in both West and East Germany, and some of the materials are in German.

Series VIII, Writings (1974-2007) includes published writings, including "Phillip Agee's Peregrinations-His Account," "Gulf War Launches New World Order," and book reviews; unpublished Writings, including the book-length "The CIA for Beginners: 100 Questions and Answers," and "The Blond Who Spied on Me"; interviews with Agee (press, radio, documentary); speeches, including several on Latin America; reviews of Agee's writings; writings about Agee; and writings by others that were of interest to Agee.