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The collection is divided into four main groups: The first group contains papers relating to William Clift's work as conservator of the Hunterian Museum. This is the largest of the four groups and contains a number of sub divisions such as explanation and display of specimens, expanding the collections, administration of the museum, and correspondence. This group also contains the transcripts made by Clift and others of the Hunterian manuscripts. The second group contains work carried out by William Clift as an illustrator for publications. The third group contains a small amount of personal material that is in the collection. The fourth group contains transcripts and copies of manuscript material by William Clift that is held in other repositories such as the Natural History Museum.

The Institute's records are arranged as follows: Director's books and associated records of post mortem examinations, 1907-200, including Bethnal Green and Mile End Hospitals autopsies, 1969 - 1978 and indexes 1907 - 1967; Surgical Department Director's books 1909 - 1995, including indexes 1909 - 1982; Cytology Department registers, 1966-1982; Bethnal Green Hospital Surgical Department records, 1972-1976; Mile End Hospital Surgical Department records, 1972-1982; Mile End Hospital Cytology Department records, 1969-1981; Specimen books, 1923-1934; Photographs and slides, 1959 - 1980; Classification schemes and indexes, 1907-1981; Publications, 1906 - 1979.

Administrative records, chaplaincy records, clinico-pathological minute books, title deeds and other legal records, financial records, patient records, nursing records, photographs and records received from unofficial sources.