Autoimmune Disorder The body’s immune system, which normally fights off diseases, mistakenly attacks a part of its own reproductive system. This hurts the ovaries and prevents them from making female hormones (estrogen, progesterone) that regulate the reproductive system.Chromosomal Irregularity Some cases of early menopause are caused by defects on an X chromosome, also known as “fragile X syndrome”. Women have two X chromosomes and even though only one of these chromosomes is active, a defect on either one can cause early menopause.