Shahid graduated with a degree in Parasitology from the University of Glasgow, after which he worked as a Research Assistant in the Institute of Molecular Medicine, University of Oxford (in the group of Chris Newbold). For his PhD he moved to the University of Cambridge, where he performed molecular genetic studies on the protozoan parasite, Toxoplasma gondii. He worked as a post-doctoral scientist at the National Institute for Medical Research (London, UK) where he examined the expansion and expression of multi-gene families involved in malaria-parasite invasion of red blood cells.