Hello and Welcome to ‘Ask A Doctor’ service. I have reviewed your query and here is my advise. Chocolate cysts in the ovary are due to endometriosis, a condition where some endometrial tissue (inner uterine layer) migrates to other areas (like ovaries) outside of the uterus. It may cause other problems like aderences which may block the uterine tubes and may contribute to infertility. You can have a test called hysterosalpingograme which check if the tubes are intact of blocked and if they are blocked and you are willing to conceive your doctor might need to do a laparoscopy (enter the low abdomen with a tube with a camera) and check for aderences of the tubes and try to release them. Hope I have answered your query. Let me know if I can assist you further.