Macrobid can darken your urine. The dark color is not indicative of any problems. From my personal experience (and everyone is different) for me this indicates I'm not taking it properly. Macrobid works best when taken with a meal. I have read studies that indicate its bioavailability increases by about 40%. If I take it with food (like I'm supposed to) it does not darken my urine. If I take it on an empty stomach, my urine is more likely to be dark. Also, don't take it within a few hours of taking anything for heartburn. Some heartburn meds (particularly those containing magnesium trisilicate) reduce the effectiveness.
See the following on Macrobid:
http://www.rxlist.com/cgi/generic/nitro25m_cp.htm
http://www.truestarhealth.com/Notes/1445008.htm
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