The papers of Theophilus Wylie have been organized into ten series: Correspondence; Diaries; Research notes and notebooks; Administrative files; Ledgers and financial materials; Indiana University history research; Sermons, lectures and public addresses; Writings and publications; Library; and Drawings.

The Correspondence series is described at the item level and is arranged in chronological order, spanning 1830-1895. Frequent correspondents include brother Theodorus William John Wylie (TWJW), Rebecca Dennis, who becomes his wife in 1838, and various Indiana University faculty and trustees.

The Diaries series contains both the original diaries kept by Theophilus Wylie during his lifetime and a sub-series of transcriptions of those diaries done by Elizabeth Greene in the 1980s. The transcriptions also contain translations of the Greek and Latin sections of the original diaries. Highlights of the diaries include passages concerning the specific goings on around the Indiana University campus from 1837 through Wylie's retirement in 1886, including the fire of 1883 which resulted in the re-location of the university to its current location east of Seminary Square at Dunn's Woods. The Addenda consists of material discovered after the initial transcription of the Wylie diaries. Each sub-series has been arranged in chronological order.

The Research notes and notebooks series consists of material gathered by Wylie while conducting various scientific investigations or as he was pursuing his own personal interests. The series is arranged in chronological order and consists primarily of his notebooks containing numerous chemistry and mathematical calculations.

The Administrative files series contains documents created by Wylie in the performance of various official duties. This series has been arranged in alphabetical order by folder heading and is further organized into three sub-series: General administrative files, Interim presidential files, and Church records. The Interim presidential files cover Wylie's short tenure as interim president after William Daily's departure in 1859. Included in this sub-series are records concerning purchases for the university library, his class attendance records, reports, draft resolutions drawn up by the university faculty, a baccalaureate address to the senior class, and documentation dealing with the senior exams in 1859. The Church records sub-series contains the minutes of the Monroe County Bible Society, the membership roster of Reformed Presbyterian Church from 1840-1857 and a document detailing the transfer of church property to the United Presbyterian Church circa 1872.

The Ledgers and financial material series is comprised of material relating to financial transactions undertaken by Wylie. The series is arranged in chronological order, with the second half of the collection documenting the running of the household at Wylie house, which is now a historic landmark registered with the National Register of Historic Places. The Indiana University history research series chronicles Wylie's work on his publication Indiana University, its history from 1820, when founded, to 1890.Included in this series are lists of IU alumni, faculty members, and administrators. This series is arranged in alphabetical order.

The Sermons, lectures, and public addresses series comprise all of the surviving public speeches Wylie gave during his lifetime. The bulk of the series consists of religious sermons delivered by Wylie as pastor of the Reformed Presbyterian Church in Bloomington, Indiana. Most are fully written out addresses but in some instances, there are simply notes that he most likely later turned into full addresses. The first subseries, By Subject, are arranged in chronological order. The second subseries includes lectures by Wylie based on the books of the Bible, and is arranged according to the book's placement in the Bible. The bulk of this material deals with the book of Psalms, the book of Matthew, and the book of Revelation. This subseries also includes un-translated passages in both Greek and Latin.

The Writings and publications series is one of the smaller series in the collection and is comprised primarily of poetry written by Wylie. The series is arranged in alphabetical order by title of the work.

The Library series contains material documenting the development and growth of Wylie's personal library, which was donated to Indiana University by the Boisen Family when ownership of Wylie house was transferred to the University. Today the complete book collection can be accessed at Wylie house by appointment. In this series there is a list of books that comprise the collection found at Wylie house, and a piece written by Anton Boisen about the history of the library. Also found in this series is a sub-series of pamphlets collected by Wylie and assumed to have been part of his library; contained therein are catalogues from other institutions and assorted published lectures. The series is arranged in alphabetical order.

The Drawings series consists of drawings rendered by Theophilus Wylie. An accomplished artist in his spare time, Wylie frequently drew renditions of his surroundings at Wylie House, in Bloomington, and of his interpretations of the political climate of the time. Items of interest in this series include a political cartoon entitled "Major Jack Downing his Vision," various images of Wylie House, and a drawing of the university campus in its former location at Seminary Square before the fire of 1883. This series is arranged in alphabetical order.

The final series, Ephemera, consists of odds and ends collected by TAW -- newspaper clippings, recipes, menus, etc.