Some folks have reported noticing an unusual (and most unpleasant!) odor in their urine during Phase 2 (Burn). This may have several causes. Personally, my wife, Susan, and I couldn't figure out what was going on until we made this connection: asparagus!
Did you eat asparagus? If so, the odor, while pungent, is normal. Asparagus causes an ...how to put this... "unique aroma" to one's urine. I'd wager that this is what's going on. If not, it could also be due to the general effect of the process of ketosis (fat-burning) or detoxing--your body is ridding itself of the legacy fat cells and all of their contents. It does this any number of ways, via sweating or rashes or acne breakouts (remember, our skin is our largest organ).
If none of this seems to be the case, consult your physician as breakouts and unusual odors are somewhat atypical (unless, as mentioned, you've eaten asparagus). Odors can often be signs that something else may be going on, so if the condition persists, seek medical attention.
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