While this page of links focuses on special collections, kudos are due to librarians at the State Historical Society of Wisconsin, New York Public Library, and Minneapolis Community and Technical College for collecting zines and other alternative periodicals and mainstreaming them as part of whole collections:
Amateur Newspaper Collection, American Antiquarian Society (Scope: 19th century)
Bowling Green University Popular Culture Library
Canadian Lesbian and Gay Archives
Centre International de Recherches sur l'Anarchisme (CIRA)
Comic Art Collection, Michigan State University Libraries
Commonweal Collection ("An independent specialist library concerned with... non-violent social change," located at Bradford University, UK)
Durland Alternatives Library (Cornell University)
New York State Library Manuscripts and Special Collections (Includes Mike Gunderloy's archives, also known as the Factsheet Five collection; focus: zines circa 1982-1992)
56a Infoshop Archive (London, UK)
Franklin and Penelope Rosemont Collection of
IWW Publications and Ephemera (Newberry Library, Chicago)
Holt Labor Library (San Francisco-based labor and radical history library)
Independent Publishing Resource Center (Portland, OR)
Kate Sharpley Library (London-based depository of anarchist history)
Kinsey Institute Library & Special Collections (not open to the general public)
Labadie Collection, University of Michigan (anarchism and radicalism) ..
Manuscripts in the Labadie Collection (Guide to the Collections, including papers of Joseph Labadie, Emma Goldman, Voltairine de Cleyre, Ammon Hennacy, Fifth Estate, Wendell Philips, Josiah Warren, National Transgender Library & Archive) ..
"Keeping Anarchy in Order" (article about Julie Herrada and the Labadie Collection, Michigan Today, Spring 2002)
Little Magazine Collection, University of Wisconsin
Michigan State University American Radicalism Collection (anarchism and radicalism)
The Moore Collection of Underground Comix (located at Cal-Poly)
Niebyl-Proctor Marxist Library for Social Research
ONE Institute ("World's largest research library on Gay, Lesbian, Bisexual, and Transgendered heritage and concerns"; based in Los Angeles and open to the public)
Prelinger Library (San Francisco)
Quatrefoil Library (St. Paul-based gay, lesbian, bisexual, transgender collection)
Sallie Bingham Center for Women's History and Culture (Duke University Rare Book, Manuscript, and Special Collections Library)
San Francisco Public Library's Little Maga/Zine Collection
Schlesinger Library (focus: U.S. women's history since the early 19th century; part of Harvard's Radcliffe Institute, it's open to the public)
Human Sexuality Collection, Cornell University (focus: "U.S. lesbian and gay history and the politics of pornography")
Sexuality Libraries, Archives and Collections (links from Cynde Moya)
Sophia Smith Collection (Women's history manuscripts, Smith College Library)
Southern California Library for Social Studies and Research
SUNY-Buffalo Library, Poetry/Rare Books Collection
Tamiment Institute Library & Robert F. Wagner Labor Archives (recent acquisition: Abraham Lincoln Brigade archives)
Temple University Libraries Contemporary Culture Collection
Univ. of Connecticut Library alternative press collection
Walter P. Reuther Library of Labor and Urban Affairs (Wayne State University)
Working Class Movement Library (Salford, England)
Jenna Freedman's "Zines in Libraries" links
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