Hello dear, I understand your concern. In my opinion the brown discharge can be due to various reasons like:- 1)Vaginitis-vaginal infections 2)Cervicitis-Cervical inflammation 3)Pelvic inflammatory disease 4)Implantation bleeding 5)Birth control pills etc. Mostly in the vaginitis and cervicitis the brown discharge is associated with vaginal irritation and itching and is associated with foul smell. And the discharge might be present throughout the cycle. But in your case as the discharge is not present throughout the cycle and not associated with irritation. So it might suggest implantation bleeding in case of pregnancy. But it is confirmed by doing a urine pregnancy test a week after missed period. So wait and check for the period. In the absence of pregnancy it might be attributed to hormonal imbalance. Nothing to worry. Hope this helps. Best regards...Dr.Srilatha