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I am too experiencing back pain from a ovarian cyst currently. It can be from a large cyst because the cyst I am dealing with right now is 9cm+. But then again, I am no doctor, but my doctor's have told me many times it is from my cyst. Your period is irregular with a cyst and taking birth control. I take Yaz. Even though I'm only 15 I understand your concern. Get a ultrasound just to be safe. I get ultrasound's every 2 weeks because my cyst is being monitored because the birth control does not shrink my cyst. It might be the same case as for you. Some times birth control does not help cysts.