Gordon has extensive teaching experience at both the undergraduate and postgraduate level. He has served on several editorial boards and regularly reviews manuscripts for high-impact journals. He is a consultant for industry and has founded biotechnology companies, including the single-chain antibody company VHSquared.

Gordon is a Fellow of the Royal Society, the Biology Society, the Academy of Medical Sciences and is an EMBO (European Molecular Biology Organization) member. He established the Centre for Molecular Microbiology and Infection (including a raising funding for a building) at Imperial College London and was the Board of Management representative for Pathogen Research for ten years (2004-2014) at the Sanger Institute where he is currently a Senior Group Leader.

Current position
Gordon is currently a Senior Group Leader at the Sanger Institute. His research focuses on the use of genomics to study host/pathogen interactions during infection. The team consists of 10-15 individuals including core scientists (in vivo, FACS (Fluorescence-activated cell sorting) and microscopy), Postdoctoral Fellows and PhD students.

On joining the Sanger Institute in 2004, Gordon reshaped the science, building new facilities and recruiting new Faculty. He nurtured links with the internal Mouse and Human Genetics programmes and established a global network of collaborators built around open-access policies. Gordon's current Faculty research investigates host/pathogen interactions associated with enteric bacterial pathogens, principally S. enterica serovar Typhi. He also directs other projects investigating the genetics of host susceptibility to infection through mouse and zebrafish infection screens.

Industry and International work
Gordon worked for more than ten years for the multi-national pharmaceutical company, The Wellcome Foundation, which is now part of GSK. During this period he became Head of Molecular Biology, managing teams working on vaccines, humanised antibodies and scale-up systems. He contributed to the discovery of pertactin as a key protective antigen for acellular whooping cough vaccines and is now an advisor for many companies, serving as an Scientific Advisory Board (SAB) or Board member. Gordon was Chair of the SAB for Novartis Vaccines & Diagnostics for more than ten years and helped found the Novartis Vaccine Global Health Institute (NVGH).
He is currently on the board of The Hilleman Laboratories, a joint enterprise between Merck and The Wellcome Trust and has founded spin-out companies and served as a Trustee at the International Vaccine Institute in Korea. Gordon is also currently an SAB member for ICDDR-B (International Centre for Diarrhoeal Disease Research, Bangladesh) and has served as a member of several WHO (World Health Organization) Committees.