The papers of Harold Pepinsky are organized into ten series: Education; Indiana University; Publications; Case files; Correspondence; Subject files; Collected materials; Awards; Audiovisual materials; and Computer disks.

The first series, Education, is arranged chronologically and includes materials from Pepinsky's educational career, beginning with high school and going through his time at Harvard Law School. Included are course readers prepared by Harvard professor Thomas Ehrlich, who went on to become the 15th president of Indiana University (1987-1994).

The second series, Indiana University, is further organized into two sub-series: Administrative and Teaching. Arranged alphabetically by folder title, the administrative materials focus on the Department of Criminal Justice and include materials such as department handouts, academic enhancement planning documents, undergraduate newsletters, and Ph.D. program summaries. Also arranged alphabetically, the teaching materials include a variety of materials such as course handouts, course syllabi, student dissertations and master theses, lecture notes and course readers for courses such as seminars on feminist justice and alternative social control systems.

Arranged chronologically, the Publication series consists of a variety of publications such as book reviews, journal submissions, articles, conference presentations, and monographs written by Pepinsky as well as outside reviews of Pepinsky's work. Included within this series are working versions of Myths That Cause Crime, The Geometry of Violence and Democracy and Criminology as Peacemaking.

Arranged alphabetically, the Case files series consists of records related to legal cases Pepinsky used as examples in his classes and includes court documents, news articles, and psychological reports. The cases, from local to international, cover a wide range of crimes, including murder, abuse and kidnapping.

The fifth series, Correspondence, is further organized into three subseries, Personal, Prisoner, and General correspondence. Arranged alphabetically, the personal correspondence consist primarily of correspondence with colleagues, professional organizations, and individuals who presented in courses taught by Pepinsky. Also included are emails printed from the 3 ½ floppy discs, now located in the Computer disks series. The prisoner correspondence is arranged alphabetically by surname, and consists of correspondence between Pepinsky and incarcerated individuals. The correspondence with the prisoners was often initiated by Pepinsky in order to gain a greater perspective of the realities of the penal system and to provide the prisoners with an emotional support system. Pepinsky did not provide any significant legal advice to the prisoners but did assist with petitions. Arranged chronologically, the general correspondence sub-series consists of correspondence with colleagues, individuals seeking his advice, guest speakers for Pepinsky's classes, mass emails on mind control, and professional and non-professional organization related correspondence.

The sixth series, Subject files, is arranged alphabetically by folder title and consists of a wide variety of subjects, including conferences and presentations; professional organizations; informational materials related to research interests, such as fact sheets, newsletters, and papers; and CVs and works of colleagues.

The Collected materials series is further organized into two subseries, Clippings and newsletters and Papers. Arranged alphabetically, the Clippings and newsletters subseries consists of material related to Pepinsky's research interests, such as prison reform, peacemaking, abuse and violence, and drug reform. Arranged alphabetically by author's surname, the Papers subseries consist of master theses, dissertations, articles and manuscripts written by individuals not associated with IU. The topics of the papers are related to his varied research interests, such as abuse and violence, prison reform, peacemaking, and satanic ritual abuse.

The eighth series, Awards, is arranged alphabetically and consists of awards in paper certificate and plaque forms that Pepinsky received for his professional and volunteer activities.

The ninth series, Audiovisual materials, is arranged alphabetically and consists of a wide range of materials, such as videotaped class lectures and presentations, documentary materials for teaching purposes, and videotaped professional organization meetings, all on a variety of formats, such as U-Matic, VHS, DVD and cassette tape.

The final series, Computer disks, consists of a variety of information and files stored on 3 ½ floppy discs and CD-ROMs that included email correspondence with colleagues and students, correspondence for organizations such as the Bloomington Faculty Council and ICOPA, papers, and course and student information and correspondence. Any information on the discs that could be accessed was printed and arranged in the relevant series, but a large portion was not printed due to inaccessibility due to software incompatibility.

This series also includes an external hard drive with a significant amount of material. The material on this hard drive includes course handouts, syllabi and correspondence with students. It also includes personal correspondence and correspondence with prisoners, C.V.s and drafts of publications and papers. Materials relating to students, including correspondence and student papers are restricted.