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Have these headaches been diagnosed as Migraines? It's important to know that bad headaches aren't necessarily Migraines.
As for why any antibiotic gives you a bad headache, this is a question you need to ask your doctor. I looked up several antibiotics, thinking that headache might be a common side effect, but it wasn't.
This is definitely a problem you should discuss with your doctor though. When you have an infection and need an antibiotic, it's important to take the entrire cycle.
Please let me know what you find out?