Abernethy Library, Middlebury College, Middlebury, Vermont
http://www.middlebury.edu/academics/lis
Has numerous Thoreau manuscripts including letters and poems. Also has numerous volumes from Thoreau's personal library, Thoreau relics, Helen Thoreau's scrapbooks, and a large collection of books by and about Thoreau.
American Antiquarian Society, 185 Salisbury Street, Worcester, Massachusetts
http://www.americanantiquarian.org
A national research library of pre-twentieth century American history and culture.
Concord Free Public Library, Special Collections, 129 Main Street, Concord, Massachusetts
http://www.concordlibrary.org/scollect/scoll.html
The most comprehensive archive of primary and secondary source material related to Concord history, life, landscape, literature, people, and influence from 1635 to the present day. Contains Thoreau manuscripts, letters, property surveys, books from Thoreau's collection, and a variety of Thoreauviana. Henry's surveying equipment is on permanent display.
Concord Museum, 200 Lexington Road, Concord, Massachusetts
http://www.concordmuseum.org
Brings all facets of Concord's history to life. Emerson's study, Thoreau's desk, chair, and flute are on permanent display. Additional pieces of Thoreauviana can be seen here.
The Henry W. and Albert A. Berg Collection, New York Public Library, Room 320,
Fifth Avenue and 42nd Street, New York, New York
http://www.nypl.org/research/chss/spe/brg/berg.html
Has the largest collection of manuscripts of Thoreau letters and also many unpublished manuscripts of nature notes and charts. Includes many first editions of Thoreau's works, including a number of autographed presentation copies from Thoreau to his friends and distinguished contemporaries.
Houghton Library, Harvard University, Cambridge, Massachusetts
http://hcl.harvard.edu/libraries/#houghton
Has a large collection of Thoreau manuscripts, including letters and rough drafts of several essays. Also has records of the Harvard Class of 1837, which Thoreau graduated with. Thoreau's herbarium is in the Agassiz Museum at Harvard.
The Huntington Library, 1151 Oxford Road, San Marino, California
http://www.huntington.org
Houses the manuscripts of many of Thoreau's poems and letters, fragments from his journal, the rough drafts of Walden, the Minnesota journal, and other miscellaneous manuscripts.
Massachusetts Historical Society, 1154 Boyleston Street, Boston, Massachusetts
http://www.masshist.org
A major research library and manuscript repository that collects, preserves, and communicates historical information about Massachusetts and the nation to the widest possible audience.
The Morgan Library & Museum, 225 Madison Avenue, New York, New York
http://www.themorgan.org
Contains the manuscript of 95% of Thoreau's journal, his unpublished Indian and Canadian notebooks, and many other manuscripts.
The Thoreau Institute, 44 Baker Farm, Lincoln, Massachusetts
http://www.walden.org/Institute/Collections/LibraryInformation.htm
Provides the most comprehensive body of Thoreau-related material in one place. Houses the collections of the Thoreau Society, the Emerson Society, and the Walden Woods Project, including the research collections of Walter Harding, Raymond Adams, Roland Robbins, and Edmund Schofield, among others. Contains Thoreau manuscripts, surveys, the "Calvin Greene" Maxham daguerreotype, and other items related to Thoreau and his circle.

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