Cyst in uterus and also endometriosis can cause infertility. This problem should be treated in order to get pregnant. The clomid is only ovulation inducer. It will induce the ovulation only, If ovulation take place by clomid, then your uterus will not be prepared for implantation due to cyst. So you should not use clomid until get fully recovered from cysts and endometriosis.