I was cramping and then brown vaginal discharge came. what can be the cause of that?

Break through?: It almost assuredly came from inside the uterus, thus the cramps. The uterus cramps when it is in process of flushing or cleansing itself. What is discharged is usually the menstral lining mixed with blood. Other things that the uterus wants to discharge are recent products of pregnancy, a polyp, or fibroid. This is usually accompanied by blood and old blood is brown.