Synaesthesia is a condition in which stimulation of a sensory modality evokes another sensation in the same or a different sensory modality. Currently, synaesthesia is considered a neurological condition that involves crosstalk between brain regions. Given the numerous anatomical and functional connections within the brain, it is possible that undiagnosed synaesthesia may influence the results of functional magnetic resonance imaging (fMRI) studies or even structural MRI. In this paper, we investigated the currently available literature to determine if and how the sensations invoked by synaesthesia could impact fMRI and structural MRI. Our investigation found that synaesthesia can have a profound impact on fMRI studies of sensory and cognitive functions, and there is evidence to suggest structural connections in the brain are also altered. Given the low prevalence of synaesthesia, the likelihood of synaesthesia being a confounding factor in fMRI studies of patient groups is small; however, determining the presence of synaesthesia is important for investigating individual patients.