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1 If the liver is unable to break down the ammonia it is excreted in the urine.  Other diseases - Other common causes of the ammonia smell in urine are diabetes, metabolic disorders, sexually transmitted diseases, medications, vitamins, and nutritional supplements.
As urea is excreted, excess nitrogen in the body goes out with it. Urea is actually solid, colorless and odorless. However, it can give off ammonia in the presence of water. The ammonia gives the strong odor in the urine.