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During the 1970s he worked closely with Sidney Pollard producing three volumes of documents covering European Economic History in the modern period. These books were: The Process of Industrialization (1968); Industrial Power and National Rivalry (1972) and The End of the Old Europe (1973). Holmes and Pollard also edited Essays in the Economic and Social History of South Yorkshire (1977 reprinted 1979). Together with Alan Booth, in 1991 Holmes edited and contributed to a "festschrift" for Pollard called Economy and Society. European Industrialisation and its Social Consequences. On Pollard's death in 1988 Holmes became his literary executor and also edited for publication Pollard's Essays on the Industrial Revolution in Britain (2000).

However, he is best known for his work on British antisemitism, migration and fascism. His first major contribution to this field was an edited volume, Immigrants and Minorities in British Society to which he contributed an essay on 'J.A.Hobson and the Jews'. In 1979 Holmes wrote Anti-Semitism in British Society 1876–1939, which proved to be an inspiration for the growth of research into the area of fascism and antisemitism. He also wrote influential articles on the British editions of the notorious Protocols of Zion. Holmes jointly founded the journal Immigrants and Minorities in 1981 and served as joint editor until 2011. He currently sits on its advisory panel.

In 1998 he wrote John Bull's Island: Immigration & British Society, 1871–1971, which is widely regarded as the authoritative text on the history of migration. It focused on a wide range of groups that entered Britain in these years, their contributions to society and the varied responses they encountered. A similar but smaller study, A Tolerant Country? Immigrants, Refugees and Minorities in Britain, appeared in 1991. Holmes's interest in migrant groups was also evident in his contribution, 'The Chinese Connection' which appeared in Outsiders & Outcasts. Essays in honour of William J Fishman (1983) which he edited jointly with Geoffrey Alderman, and his two volumes of edited source material in Migration in European History. He contributed on 'British Government Policy Towards War Time Refugees' in M. Conway and J Gotovitch Europe in Exile. European Exile Communities in Britain, 1940–1945 (2001). In 2008 'The Burton Book' co-written by Geoffrey Alderman appeared in the Journal of the Royal Asiatic Society. In 2015 his chapter 'William Joyce and the German Connection' was published in Ian Wallace (ed.) Voices from Exile (Leiden and Boston, 2015). Much of his time recently had been consumed by working on his long-awaited and widely regarded as definitive political biography of William Joyce: Searching for Lord Haw-Haw: The Political Lives of William Joyce, which was published by Routledge in 2016. An East End Legacy: Essays in Memory of William J.Fishman, edited with Anne J. Kershen appeared in 2017. The following year he was presented with a “festschrift,” called Migrant Britain, edited by Jenifer Craig-Norton, Christhard Goffman and Tony Kushner. His latest publication is Chapters of Accidents. A Writers Memoir, edited with Nick Baron and published in 2022.

During his career Holmes supervised a large number of postgraduate students, some of whom have subsequently been appointed to Chairs in British Universities, and who are often referred to as the "91ֱ�� School" (see Welsh History Review, June 1990. vol. 50. no. 1. p. 138). Following his retirement, in 2002 he held a Parkes Fellowship at the University of Southampton.