You may have temporary malabsorption during a bout of stomach flu, but malabsorption disorders that last a long time occur from an underlying condition that you've had for a long time. Malabsorption has many causes, but they fall into a few general categories.

Damage to the lining of the small intestine

Your small intestine is where most of your nutrient absorption happens. (A small amount happens in your large intestine). The mucous lining of your intestinal walls is involved in both secreting digestive enzymes and absorbing liquefied food into your bloodstream. But inflammation (enteritis) and injury can damage this mucous membrane. The damage can be temporary (acute) or long-lasting (chronic). Some causes include:

• Infectious diseases such as Whipple's disease and tropical sprue.

• Inflammatory bowel diseases such as ulcerative colitis and Crohn's disease.

• Autoimmune diseases such as cellac disease.

• Overuse of certain drugs and medications.

• Alcohol use disorder.

• Radiation therapy and chemotherapy.

• Short bowel syndrome.

• Small intestinal bacterial overgrowth (SIBO).

• Overproduction of stomach acid, as in Zollinger Ellison syndrome.

Pancreas, gallbladder and liver diseases

Your pancreas, liver and gallbladder all work together with the small intestine to break down food. Your pancreas makes important digestive enzymes, while your liver and gallbladder make and store bile, which is important for digesting fats. These organs deliver their substances to your small intestine when food is present. But if a disease stops them from doing their jobs, your small intestine won't be able to break food down enough to absorb it. Examples include:

• Pancreatic insufficiency.

• Cystic fibrosis.

• Bile duct blockages.

• Gallbladder diseases.

• Liver disease.

Lymphatic system diseases

Your small intestine absorbs fats into your bloodstream through lymph vessels. Diseases of the lymphatic system that block these vessels can compromise the absorption of fats. Intestinal lymphangiectasia and lymphoma are two examples of this.

Food intolerances

Malabsorption of certain carbohydrates or proteins can occur as a side effect of gastrointestinal disease. (Fructose malabsorption is a common example.) But sometimes people are born lacking the necessary enzymes to break down certain nutrients. (Lactose intolerance is the most common example of this.)