Smelly brown urine can be caused by acute viral hepatitis, cirrhosis of the liver and a urinary tract infection, according to MedlinePlus. The brown color is caused by liver disease, while the smell comes from a urinary tract infection.
The brown color occurs because the body is producing too much bilirubin in response to the disease, says MedlinePlus. Bilirubin is a brown-yellow material that is found in bile. It's made when the liver destroys red blood cells and is normally passed out of the body through feces.
More benign causes of lighter brown urine can be ingesting blackberries, beets or foods that have been artificially colored, says MedlinePlus. Medications also cause brown urine, but it can also be caused by hemolytic anemia, porphyria, injuries to or diseases of the urinary tract that lead to bleeding and injuries to the kidneys.
Hemolytic anemia happens when red blood cells are prematurely destroyed, says MedlinePlus. This is caused by such inherited disorders as sickle cell anemia, though infection and exposure to toxins can also cause it. Porphyria is an unhealthy buildup of porphyrins, claims Mayo Clinic. These are chemicals that support the actions of hemoglobin, which carries oxygen to the cells of the body.
Abnormal urine that doesn't go away after time needs medical attention, says MedlinePlus.