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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.
An ammonia test measures the amount of ammonia in the blood. Most ammonia in the body forms when protein is broken down by bacteria in the intestines. The liver normally converts ammonia into urea, which is then eliminated in urine. Ammonia levels in the blood rise when the liver is not able to convert ammonia to urea.