The papers contain much relating to the administration of the University of St Andrews as well as to Donaldson's academic interests in classical studies and theology. They comprise his personal correspondence, as well as notes, scrapbooks, offprints and a fine series of photograph albums:
- ms5600-9012: Correspondence, 1859-1912
- ms29951/1-10 Photograph albums (see more detailed description below)
- ms29952/1-19 Boxed series (listed) including executry papers; miscellaneous personal papers; newspaper cuttings; University addresses and articles, 1891-1914; Addresses and other papers; mixed personal, family, academic and official papers, lectures, addresses, and correspondence including relating to other Scottish universities and university administration, 1845-1914; Papers relating to university appointments, Dundee question, women in the university, special lectureships, benefactions, college church, bursaries, scholarships, university teaching and teachers, examinations etc.
- ms29953/1-10 Correspondence with C Stuart Grace, Secretary of the University, 1890-1898 and with others including on admission of women students 1892, LLA scheme and University Hall 1888-1900, Berry Bequest 1889-90, SRC over student representative on court 1892
- ms29954 Correspondence file, letters to Donaldson and autographs, 1880-1916
- ms29955/1-9 Small volumes
- ms29956/1-16 Small volumes
- ms29957/1-107 Notebooks, diaries etc. including lists of school pupils at Edinburgh Royal High School and Stirling High School, on classical and patristic subjects, and on University of St Andrews and University of Aberdeen, 1846-1915
- ms29958 Diaries, 1879 onwards
- ms29959 Papers relating to general councils, official university business
- ms29960/1-12 Newspaper cuttings albums
- ms29961 Volumes (46) of which 20-25, 30-33 are listed: Bound volumes containing papers and copies of documents relating to the administration of the University, university finance, reports on student numbers and new ventures including the Gatty Marine Laboratory and the Botanic Garden, correspondence, ordinances etc., 1884-1910 (with copies of earlier documents from 1840)
- ms29962 Papers relating to official university business
- ms29963/1-37 Printed papers, 1863-1920
- ms29964/1-19 Press cuttings and correspondence, 1848-1915
- ms29965/1-35 Diaries, 1854, 1881-1905
- ms29966/1-13 Photographs and postcards, ca. 1850-1938.