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The JCMA maintains a collection of over 1200 objects, predominantly two-dimensional works. At its core is the Stottlemyer collection, a 1998 gift to Juniata College by Quayton Stottlemyer, Juniata College class of 1951, in honor of his father. Acquisition of this large and varied collection spurred the development of the Museum and the renovation of exhibition spaces in Carnegie Hall to accommodate presentation of both permanent collection objects and temporary exhibitions. Since that time, the JCMA collection has expanded through gifts and strategic purchases to provide students and the surrounding community with opportunities to consider the breadth and diversity of human expression through artistic endeavor. Most recently, the JCMA received a gift of over 400 works on paper from Robert Wagoner, a former professor of Philosophy at Juniata College. 

Key holdings in the painting collection include American landscapes from the Hudson River School, still lifes and portraits; small-scale European genre scenes of the 17th – 19th centuries; a collection of 18th – 20th century portrait miniatures; and Modern and Contemporary works by Günther Spaltmann, Robert Birmelin, Romare Bearden, and Richard Mayhew.

Works on paper showcase a variety of techniques, including etchings by such well-known artists as Rembrandt, James McNeil Whistler, and Pablo Picasso; drawings and watercolors by the 19th century American artists Thomas and Edward Moran; Japanese woodblock prints by Kunisada and Hiroshige; oil color lithographs by George Baxter; print illustrations for Historic Churches of America (1890); and a growing collection of contemporary works.

Juniata College is home to The Peace Chapel, a site-specific environmental work designed by artist/architect Maya Lin in 1988-89. Located on a hillside just east of campus, the Chapel is open to the public and is accessible by marked walking trails.