I feel your pain.
I had ovarian cysts a few years ago. I didn't know it was that until I ended up with unstoppable pain in the hospital.
They were follicular (liquid) cysts and a dermoid (solid) cysts. About a month later I had the dermoid and the biggest follicular taken away by laparoscopy. A smaller follicular stayed there. They don't usually take cysts away unless they're bigger than 5 cm, because the surgery causes more risks than the cysts themselves.
If I had follicular cysts, that meant that I still ovulated although I was already on the birth control pill. So I got prescribed a stronger pill (from Alesse 20 u to Minestrin which is 25 u I think) but that didn't do it: about a year later I still had cysts. Like you, I could feel them when doing impact sports (running and high-impact aerobics), just like the first time. Another trigger for pain was wearing heeled boots to walk to school (about 2 km at a fast pace), which twice hurt me enough to make me stop on a park bench to cry along my commute to the university.
So I had another ultrasound to confirm that the cysts were still there and growing (follicular, not dermoid) and my gynecological surgeon - a wonderful woman - told me she didn't want to see me in the OR again so she increased the strength of my pill again from Minestrin to Marvelon (35 units). Not one problem ever since.
There were hesitations before we changed my pill the last time because there is a history of migraines in my family and I had some neurological issues (very light seizures) as a kid. However it was considered that the risk of having to undergo surgery again was much higher than that of increasing the pill.
Maybe you should seek a second opinion. There is definitely something that can be done about your condition and it's not necessarily about pain killers.



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