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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.
Urinary ammonia is an even less reliable method for testing for CBS upregulation. This is because most of the ammonia (NH4+) in urine is produced by the kidneys for ph regulation. The ammonia that is produced elsewhere in the body, is usually detoxified by being converted to urea, which is then excreted.