Malabsorption can be caused by a wide variety of medical conditions and diseases. Impairments of digestive or absorption processes, or problems with the transport of nutrients into the bloodstream can lead to malabsorption.

The many possible causes of malabsorption can be categorized as being the result of:

• Biochemical/enzyme deficiency. When the body lacks specific chemicals or enzymes necessary for the process of digestion. For example, people with lactose intolerance lack the enzyme lactase, which is necessary to digest lactose, a sugar found in dairy products. Malabsorption can also result when the pancreas is unable to produce the enzymes needed to chemically break down food (e.g., with chronic pancreatitis, cystic fibrosis, diabetes, cancer or resection surgery of the pancreas).
  
  
• Surface area loss. Occurs when a portion of the bowel is surgically removed, reducing the amount of space available for nutrient absorption. This may occur after surgical procedures such as partial bowel resection to remove diseased portions of the intestines. Short bowel syndrome involves malabsorption as the result of surface area loss in the small intestine. Surgery performed for the purpose of weight loss (e.g., bariatric surgery) may also lead to surface area loss and malabsorption.
  
  
• Bacterial overgrowth. When too much bacteria occur in one place. A large number of bacteria in the small intestine may compete for nutrients or may damage the intestinal lining, leading to malabsorption. Bacterial overgrowth is associated with many different disorders, including short bowel syndrome, intestinal obstruction, irritable bowel syndrome and Whipple disease. Prolonged use of medications used to reduce stomach acid, such as proton pump inhibitors or H2 blockers, may also cause malabsorption as a result of bacterial overgrowth.
  
  
• Mucosal (mucous) abnormalities. When disease or abnormalities affect the mucosal lining of the small intestine, its ability to absorb or secrete substances during digestion becomes impaired, causing malabsorption. Celiac disease is a common cause of impaired absorption of the intestinal lining. Crohn's disease, cancer and infection may also cause mucosal abnormalities that can lead to malabsorption.
  
  
• Lymph vessel problems. Inability or reduced ability of nutrients to move from the small intestine into the bloodstream for circulation throughout the body. Malabsorption occurs when lymph vessels that normally carry particular nutrients into the blood become enlarged or obstructed. An example of such a condition is intestinal lymphangiectasia. 

For more information on conditions that involve malabsorption, see Related disorders.