Dr. Allen is the author, co-author or co-editor of the following books:
- Black Awakening in Capitalist America: An Analytic History (1969)
- A Guide to Black Power in America: An Historical Analysis (1970)
- Reluctant Reformers: The Impact of Racism on Social Movement in the U.S. (1983) CPUSA Online - The Nature of the "White-Black Relationship"
- Brotherman: The Odyssey of Black Men in America (co-edited with Herb Boyd Interview with Herb Boyd *Writers Write - The IWJ*, reprinted 1996)
- Strong in the Struggle: My Life as a Black Labor Activist (with ILWU militant Lee Brown, 2001)
- Honoring Sergeant Carter: A Family's Journey to Uncover the Truth About an American Hero Honoring Sergeant Carter (with Allene G. Carter, 2004)
- The Port Chicago Mutiny: The Story of the Largest Mass Mutiny Trial in U.S. Naval History :: Port Chicago Survivors - History & Concept :: Heyday Books: The Port Chicago Mutiny (1989, republished 2006).