Biliary obstruction: This is the most common cause of clay-colored stool, as it leads to a lack of bile salts in the intestine, which are essential for giving stool its normal brown color. Biliary obstruction can be due to gallstones, tumors, or strictures.

Hepatitis: Inflammation of the liver can lead to a decrease in bile production, resulting in clay-colored stool.
Pancreatitis: Inflammation of the pancreas can affect the release of digestive enzymes and bile, leading to changes in stool color.
Gallbladder disease: Diseases affecting the gallbladder, such as cholecystitis, can impair the release of bile into the intestine.

Hemochromatosis: A genetic disorder leading to excessive iron absorption, which can cause liver damage and affect bile production. Missing this diagnosis can lead to severe liver damage and other complications.
Primary sclerosing cholangitis: A chronic liver disease that leads to scarring and narrowing of the bile ducts, which can cause biliary obstruction and clay-colored stool. This condition can progress to liver failure if not treated.
Ampullary cancer: A rare cancer of the ampulla of Vater, where the bile and pancreatic ducts empty into the small intestine. This can cause biliary obstruction and clay-colored stool, and is often diagnosed at a late stage.

Caroli's disease: A rare congenital disorder of the bile ducts, which can cause recurrent cholangitis and biliary obstruction, leading to clay-colored stool.
Alagille syndrome: A genetic disorder that affects the liver, heart, and other parts of the body, and can cause bile duct paucity, leading to clay-colored stool.
Bile duct atresia: A rare condition in which the bile ducts are blocked or absent, leading to a lack of bile in the intestine and clay-colored stool. This condition is usually diagnosed in infancy.