In spite of being the oldest neurological disorder to be recorded in human history, the pathophysiology of migraine headache is not clear. In recent times, hereto unexplored mechanisms are being pursued to explain the disorder. Novel thinkers have ventured to associate migraine with chronic infection induced hypersensitivity. Infections such as Helicobacter pylori and Chlamydia have been found to be more common in migraine patients. We wanted to know whether there is any abnormal nasal bacterial colonization associated with migraine. Methods: As a single‑blinded, cross‑sectional, observational case–control pilot study in a tertiary government hospital neurology outpatient department in India, we analyzed the nasal bacterial flora of 27 migraine patients and ten relatives of these patients without migraine headache by nasal swab smear and culture. Results: The organisms detected in the participants were coagulase negative Staphylococcus and Staphylococcus aureus, Viridans streptococci, diphtheroids, micrococci, bacteroides, and Klebsiella by culture. Bacterial flora of the migraine patients was different from that of the controls, especially diphtheroids (migraine = 11% vs. control = 40%, P = 0.06) and micrococci (migraine = 30% versus control = 60%, P = 0.13) seem to be lower in migraineurs than in controls. Conclusions: From our pilot case–control study, although a small sample size of patients, migraineurs appear to have altered bacterial flora in their nose.