So their urine will naturally have more bilirubin. The liver is the site of bile formation. Bile contains bile salts, fatty acids, cholesterol, bilirubin, and other compounds. The components of bile are synthesized and secreted into bile ducts within the liver itself and bile is then sent to the small intestine. There are many causes of bilirubin in urine: Blockage of bile ducts due to gall stones.