Hello, I would be happy to help you with your question. Amoxicillin is not associated with cycle irregularity and it does NOT effect birth control or how it works. Certainly stress and significant illness can cause irregularity in terms of when you ovulate and thus irregular cycles. The most common cause of a delayed period that must be ruled out is pregnancy. If this is a possibility, then check a test. I hope that this helps. Thanks for visiting HCM!