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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.
Whereas most excretion of ammonia occurs across the gills of aquatic animals, mammals do excrete some ammonia in the urine. Amino groups are enzymatically transformed into glutamate, and then changed to glutamine in the liver. Glutamine can cross the kidney membranes (whereas amino acids can not).