Given a negative pregnancy test, it's likely that you aren't pregnant . Amenorrhea (the absence of menstruation) not related to spotting could be due to the persistence of a functional ovarian cyst. Functional ovarian cysts originate from follicles that don't ovulate and evolve into a hormone-producing cyst. Hormones from a cyst (estrogen) prevent menstruation. Functional cysts usually persist for 2-3 months and then disappear spontaneously. When a cyst disappears, menstruation begins and the period comes. Such a period is not a real period but manifests as spotting. You can visit your gynecologist for an vaginal ultrasound to confirm or exclude the presence of an ovarian cyst.