Hello First of all read this very carefully and I will try to answer your question in the end. Take treatment for hypothyroidism as advised. Stop all medicines , which you are taking for pcos and for pregnancy . Cysts are often caused by hormone changes. Using birth control pills can sometimes help regulate hormone levels so that the cysts can be taken care of. So consult another gynecologist ( just for pcos treatment ). Your gynae will likely want you to come back after you have been on the treatment to see if the cyst is gone( gynae will advise you treatment for pcos). At that time doctor suggest you stop using the medication or if indicated , you may need to continue it for a bit longer. Most probably your gynae will prescribe you BIRTH CONTROL PILLS . Once you stop the birth control pills , as long as there are not medical concerns, you shouldn t have any problems with future conception. Many woemn will use birth control pills for purposes other than preventing pregnancy. Then they stop taking them when they want to conceive. Here I mentioned in detail , so that you can take treatment for pcos . PCOS is the main cause of irregular menstruation or dysfunctional uterine bleeding or amenorrhea ( no bleeding or only spots). Since you are also taking metformine 500 mg , sometimes this is also advised for cyst. But first of all consult gynaecologist and get his opinion ( 2nd ). Once treated for PCOS then opt for conception . Hope this will help you.