Correspondence; invitations; notes re the Walter and Eliza Hall Institute; minutes of meetings of the Medical Faculty Board; University of Melbourne Medical School curriculum changes; roll books; attendance of lecture books; photographs of specimens; research on veneral diseases, influenza, maternal and infant welfare, and common causes of death and invalidity; publications. Also included is a pencil drawing of door of old Wilson Hall by daughter Mary, n.d.

Letters from the University of Melbourne concerning employment; his letters to The Age concerning claim to be paid for work as demonstrator and to the Premier's office re Commission to Enquire into the Sanitary Condition of Melbourne and Suburbs with progress and final reports, 1882-1889; letters concerning his trip to Europe in 1890, University business including the Dickson frauds, 1897-1904, his 1912 trip to Europe and the UK and the foundation of the University of Queensland Medical Schoool (1914). Also included are personal letters to Allen from Sir James Paget (London, 1891-1898); school reports from the Melbourne Grammar School, 1869; notes from Professor McCoy's Comparative Anatomy, Vertibrata, 1872 and General Anatomy notes, 1873; certificates for attendance at the Melbourne Hospital and for Registration; testimonials supporting appointments from E. James, S.D. Bird, G.B. Halford, T.N. Fitzgerald, James Robertson etc; his licences to practise; conferrring programs for ceremonies at which he received honours; tributes to him on his retirement and death; invitations and programs; pencil drawing of the door of Old Wilson Hall by his daughter, Mary Cecil Allen.

Paper on heart action and sounds 1860; notes, correspondence and newspaper clippings relating to snake venom antidote 1867-1894; correspondence of the Australian Institute of Anatomy concerning the Halford Oration, with texts 1928-1949.