Thomas Thomson (177–1852) is primarily remembered as the author of the textbook A System of Chemistry which dominated the British field for about 30 years. In his chosen subject of chemistry his enthusiastic support of Daltonian chemical atomism and his zealous support of Prout's hypothesis have been recently recognized. Yet his activities were not as restricted as received opinion suggests. When Thomson assumed in 1818 the newly created Regius Chair of Chemistry at the University of Glasgow, the prospects for him as teacher and researcher were apparently encouraging. But he met difficulties in his attempts to elevate the status of the Regius Professors at Glasgow and in his concurrent endeavours to develop chemistry as an autonomous science. The ensuing controversy, first private and then public, spanned more than 20 rancorous years. Only one of Thomson's obituarists, however, even briefly mentions this debate; and recent writers on Thomson either ignore it completely or skim over it lightly. The main purpose of this paper is therefore to redress the balance of previous work on Thomson by outlining the chief features of his professorial period, paying particular attention to his style of teaching and attitude to his subject. For Thomson the development of his discipline was inseparable from the question of his status as a Regius Professor. Accordingly I also try to show that he played an important role in the movement for reform of the Scottish Universities and I discuss the structure of power at the University of Glasgow. Such analysis is necessary for understanding Thomson's appraisal of his situation as Regius Professor of Chemistry. In order to put his professorial period into the context of his earlier work I introduce the main body of the article with a short reconsideration of the form and significance of his career before 1817, when he moved to Glasgow.