In short, the blood discharged during menstruation is the shed layer of the endometrium, broken down and expelled. There is a basal layer below the shed functional layer, which forms a new layer of tissue for the following month, thickening the uterine lining.hen menstruation begins, the functional surface layer of the endometrium breaks down and peels off. This is what causes bleeding during a period. Coagulation factors that would normally cause the blood to clot are instead broken down by an enzyme which is released as the endometrium breaks down.