Series 2: Subject Files, Subseries 5: Programs (1927-1994) documents a number of significant activities undertaken by the AAIA to enhance the lives of Native Americans and fulfill its mission, namely, to "sustain and perpetuate their cultures and languages; protect their sovereignty, their constitutional, legal and human rights; their natural resources; and improve their health, education, economic and community development." The programs represented in this subseries vary widely in structure and focus and attest to the Association's breadth of interest and organizational sophistication, tempered, at times, by constrained resources or human failings. While some of these programs were pursued concurrently, they also illustrate an evolution in the AAIA's agenda and environment. In the 1920s and 1930s, for example, the provision of nursing services to the Pueblo and Navajo was a major preoccupation. In the 1970s and 1980s, in contrast, maintaining the integrity of Native American families and communities through new national and local child welfare policies was a high priority.

The AAIA's activities were both practical and theoretical in nature. The latter are well-represented in this subseries in the form of conferences, workshops, and institutes which explored such issues as Native American health (six conferences were held on themes ranging from the United States Public Health Service to environmentally conditioned diseases), education, assimilation, self-government, and taxation. In addition to letters of invitation, programs, lists of participants, and the like, a number of files contain transcripts of proceedings. Among the activities which transcended the confines of the conference hall was We Shake Hands, a multifaceted program designed to help Native American communities "rediscover their power to act on their own behalf, and fulfill their desire for independence by relating themselves as political, economic and social equals to other communities of the United States," its primary constituents being the Omaha of Nebraska, the Oglala Sioux of South Dakota, and the Northern Cheyenne of Montana. Further particulars about this community-based experiment in self-assertion and cooperation can be found in the files of these tribes in Series 2, Subseries 2 (Tribal). Also worthy of note is the Indian Participation Project, which facilitated the tribal assumption on a contractual basis of operations traditionally managed by federal agencies, as well as the American Indian Arts Center, a shop which operated at various locations in Manhattan from 1963 to 1977 with the object of stimulating interest in and sales of Native American arts and crafts. In addition to correspondence, financial statements, and inventories, the files of the American Indian Arts Center contain five albums documenting various promotional activities, among them the inclusion of Native American jewelry and other accessories in the fashion pages of such magazines as Harper's Bazaar, Gentlemen's Quarterly, and Vogue.

The most substantial body of material among these files was generated by the AAIA's long-running scholarship program, which for a time was a cooperative effort with the Board for Homeland Ministries of the United Church of Christ and the National Council of the Protestant Episcopal Church. The program's beginnings were modest, but over the years it grew and ultimately provided financial assistance to hundreds of Native Americans each year. In 1990, for example, 448 awards of varying kinds were made totaling $114,425. A sample of the thousands of applications handled by the AAIA over the years has been preserved.