Our expert says:
Usually Amoxicillin won't cause a change in urine colour. Dark urine can be due to concentration, liver problems(but then it would stay dark) or blood in the urine (which will also not clear up so quickly). It could just have been that your urine was concentrated or that you ate or drank something with a colourant in it (some vitamin pills can even make your urine orange) If it stays dark for a few hours or days you need to see your doctor.
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