Synaesthesia is a neurological condition in which an inducer stimulus in one sense leads to a concurrent percept in a second sense. The immune hypothesis of synaesthesia links synaesthesia to immune-related conditions such as migraine. More specifically, migraine with aura may be linked to grapheme-colour synaesthesia as both involve cortical hyperexcitability. In this study, 188 synaesthetes and 121 non-synaesthetes completed an online questionnaire about synaesthesia and migraine. We found no general link between migraine and synaesthesia, nor between migraine with aura and grapheme-colour synaesthesia. Exploratory analyses, however, showed that certain types of synaesthetic inducer (significant: scent, emotion, and personality; trends: pain, non-lexical visual experiences, taste, and touch) were associated with visual disturbances in headache among female participants. Based on our exploratory analyses we hypothesise that specific subtypes of synaesthesia are related to migraine. The relationship between these two conditions is likely to become clearer as research on the underlying causes of synaesthesia and migraine progresses.