| RefNo | Title | Date |
| RR/7/196 | Referee's report by Allen Thomson, on a paper 'On the distribution of the fibres in the muscular tunics of the stomach in man and other mammalia' by James Bell Pettigrew | [19 June] 1872 |
| RR/3/149 | Referee's report by Allen Thomson, on a paper 'Ocular spectres, structures and functions, mutual exponents' by James Jago | 21 May 1858 |
| RR/5/183 | Second referee's report by Allen Thomson, on a paper 'On the arrangement of the muscular fibres in the ventricles of the vertebrate heart, with physiological remarks' by James Bell Pettigrew | 10 May 1864 |
| RR/7/195 | Letter from Allen Thomson, on a paper 'On the distribution of the fibres in the muscular tunics of the stomach in man and other mammalia' by James Bell Pettigrew | 19 June 1872 |
| RR/8/164 | Referee's report by Allen Thomson, on a paper 'On the effects of chloroform and ether on the radial tracing' by Charles Handfield Jones | nd [1879] |
| RR/6/225 | Referee's report by Allen Thomson, on a paper 'On the distribution of the fibres in the muscular tunics of the stomach in man and other mammalia' by James Bell Pettigrew | 7 August 1867 |
| MS/426/416 | Copy letter from C R [Charles Richard] Weld, the Assistant Secretary of the Royal Society; to Dr [John] Stenhouse | 10 April 1850 |
| EC/1848/16 | Thomson, Allen: certificate of election to the Royal Society | |
| RR/6/127 | Referee's report by Allen Thomson and Joseph Jackson Lister, on a paper 'On the development of striated muscular fibre' by Wilson Fox | 15 January 1866 |
| RR/6/298 | Referee's report by Allen Thomson, on a paper 'Observations on the development of the semilunar valves of the aorta and pulmonary artery of the heart of the chick' by Morris Tonge | 2 July 1868 |
| PT/45/3 | Paper, 'The reproduction of the ascaris mystax' by Henry Nelson | [1850] |
| RR/2/169 | Referee's report by Allen Thomson, on a paper 'Researches on the impregnation of the ovum in the amphibia; and on the early stages of development of the embryo. ( third series.)' by George Newport | September 1854 |
| RR/5/181 | Referee's report by Allen Thomson, on a paper 'On the arrangement of the muscular fibres in the ventricles of the vertebrate heart, with physiological remarks' by James Bell Pettigrew | 1860 |
| RR/3/148 | Referee's report by Allen Thomson on a paper, 'Ocular spectres, structures and functions, mutual exponents' by James Jago | 1856 |
| MS/257/2/221 | First half of letter from Robert Grant, Glasgow Observatory to Allen Thomson | 16 May 1865 |
| RR/8/85 | Referee's report by Allen Thomson, on a paper 'Points of resemblance between the suprarenal bodies of the horse and dog, and certain occasional structures in the ovary' by Charles Creighton | 14 January 1878 |
| AP/60/12 | Unpublished letter, 'Artifically formed diamonds' from James Mactear to the Secretary of the Royal Society | 14 December 1879 |
| RR/9/158 | Referee's report by Allen Thomson, on a paper 'On the development of the great omentum and transverse mesocolon' by C B Lockwood | 27 June 1883 |
| RR/9/161 | Referee's report by Allen Thomson, on a paper 'On the development of the great omentum and transverse mesocolon' by C B Lockwood | 30 October 1883 |
| MS/257/2/222 | Second half of letter from Robert Grant, Glasgow Observatory to Allen Thomson | 16 May 1865 |
| RR/8/138 | Referee's report by Allen Thomson, on a paper 'Observations on the nervous system of Aurelia aurita' by Edward Albert Sharpey-Schafer | 8 March 1878 |
| RR/2/166 | Referee's report by Allen Thomson, on a paper 'On the impregnation of the ovum, in the amphibia' [First Series], by George Newport | [1850] |
| RR/4/55 | Referee's report by Allen Thomson, on a paper 'On the relations of the vomer, ethmoid, and intermaxillary bones' by John Cleland | 3 July 1861 |