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It is possible to have unequal pupils (anisocoria) with headache disorders-migraines and cluster headaches, I believe. That doesn't mean for sure your unequal pupils are due to your headaches, or that it is benign in nature (I had unequal pupils with a Horner's syndrome back in '90 and it was the start of autonomic neuropathy for me), but anisocoria can be due to relatively benign causes such as the headaches you are describing. I would tell your doctor about it anyway.