Hello, There is no documented side effect of brown vaginal discharge after metronidazole therapy, but actually it may be flaring of underlying cervical or vaginal infection which manifest in such fashion. There can be various reasons for the same as - lack of antibiotic response from body - addition of another opportunistic infection in case of compromised immunity level - lack of hydration or personal hygiene loop hole - another infection via sex transfer (if active) - secondary infection from tampon or other foreign material. In my clinic, I recommend a culture and swab test of the discharge for fine management curative pathway. Hope I have answered your query. Let me know if I can assist you further. Regards, Dr. Bhagyesh V. Patel, General Surgeon