Yes, the most commonly prescribed medicine for bacterial vaginosis (BV) can turn your urine dark brown or reddish-brown. This is a known side effect of metronidazole (often sold as Flagyl), and while it can look alarming, the color change itself is harmless. Your urine should return to normal within a day or two after you finish your course of treatment.
Why Metronidazole Darkens Your Urine
When your body breaks down metronidazole, it produces a byproduct called an azometabolite. This metabolite carries a dark pigment that gets filtered through your kidneys and into your urine. The result is urine that looks dark brown, reddish-brown, or even close to black, depending on how concentrated it is. The darker the color, the more startling it can be, but the pigment itself has no clinical significance. It’s simply a visual side effect of how your body processes the drug.
Not everyone who takes metronidazole notices this change. The Mayo Clinic lists dark urine as a rare side effect, and some people complete a full course without seeing any color shift at all. Factors like your hydration level play a role. If you’re drinking plenty of water, the pigment is more diluted and the change may be barely noticeable. If you’re not drinking much, the urine becomes more concentrated and the color more dramatic.
Other BV Treatments and Urine Color
Metronidazole isn’t the only option for BV. Clindamycin is another antibiotic commonly prescribed, and dark urine is also listed among its possible side effects, though it’s uncommon. If you’ve been prescribed a vaginal gel or cream version of either medication, less of the drug enters your bloodstream compared to oral pills, so urine color changes are less likely with topical forms.
Nitrofurantoin, an antibiotic sometimes used for urinary tract infections that can overlap with BV treatment timing, is also known to turn urine dark brown or rusty orange. If you’re taking more than one medication, it’s worth checking whether any of them list urine discoloration as a side effect.
When Dark Urine Is Just the Medicine
The easiest way to tell that your dark urine is simply a medication side effect is the timing. If it started after you began taking metronidazole and you feel fine otherwise, the drug is almost certainly the cause. You can also expect the color to clear up within one to two days after your last dose.
A few other clues point to a harmless medication effect rather than something more serious:
- Color is consistent. The urine stays a similar shade of dark brown or reddish-brown throughout treatment, rather than suddenly changing.
- No other symptoms. You don’t have upper abdominal pain, nausea, vomiting, or yellowing of your skin or eyes.
- Stool color is normal. Pale or clay-colored stools alongside dark urine can signal a liver problem, which is a different situation entirely.
Signs That Something Else Is Going On
Dark urine can occasionally signal liver stress, and metronidazole does carry a small risk of liver-related side effects. The key difference is that liver problems come with a cluster of symptoms, not just a change in urine color. Watch for upper stomach pain or tenderness, pale stools, loss of appetite, persistent nausea or vomiting, and yellow discoloration of your eyes or skin (jaundice). If you notice any combination of these alongside dark urine, that warrants a call to your doctor.
Dehydration is another common cause of dark urine that has nothing to do with medication. If your urine is dark yellow or amber rather than brown, and you haven’t been drinking enough fluids, try increasing your water intake before assuming the medicine is responsible.
Alcohol and Metronidazole
You’ve likely been told not to drink alcohol while taking metronidazole, and this matters for more than just urine color. Combining the two can trigger flushing, headache, nausea, vomiting, and a rapid heart rate. These reactions can also include digestive symptoms that overlap with signs of liver problems, making it harder to tell what’s actually going on. Avoiding alcohol during your full course of treatment, and for at least 48 hours after your last dose, keeps things simple and reduces unnecessary side effects.
What to Expect After Treatment Ends
Once you take your last dose of metronidazole, your body clears the remaining drug and its metabolites relatively quickly. Most people see their urine return to its normal color within 24 to 48 hours. Staying well-hydrated during this window helps flush the pigment out faster. If your urine is still noticeably dark three or more days after finishing treatment, that’s worth mentioning to your healthcare provider, since at that point the medication should be fully cleared from your system.