Some ovarian cysts can be associated with decreased fertility. However, it depends on the type of ovarian cyst you have.Ovarian cysts that can affect your fertility include:Endometriomas. Endometriomas (en-doe-me-tree-O-muhs) are cysts caused by endometriosis, a condition in which the tissue normally lining your uterus (endometrium) grows outside the uterus. These ovarian cysts may be associated with fertility problems.Ovarian cysts resulting from polycystic ovary syndrome. Polycystic ovary syndrome (PCOS) is a condition marked by many small cysts on your ovaries, irregular periods and high levels of certain hormones. PCOS is associated with irregular ovulation, which may contribute to problems with fertility in some women.