Secondary lactose intolerance can be the result of several different problems all of which result in damage to the walls of the intestines. Any time a person suffers from a disease that causes damage to the intestines it reduces their ability to produce the lactase necessary to digest the lactose in dairy products.

Temporary secondary lactose intolerance can often occur after a person suffers from any form of gastroenteritis such as stomach flu, a bowel infection or even infectious diarrhea that cause inflammation of the bowels. While the bowel is inflamed, the cells that produce lactase are damaged and unable to do their job. While in this state the person is likely to be unable to tolerate most types of dairy products, if they continue to consume dairy this will only exacerbate the problem with continued bouts of diarrhea. In most cases this type of secondary lactose intolerance will go away in a couple of weeks after the person has recovered from the gastroenteritis.

In some cases a primary disease such as Celiac disease can be the cause of secondary lactose intolerance. Celiac disease causes damage to the inside lining of the intestines in people who consume gluten when they have this disease. The damage caused can be quite severe and may be permanent in some people. This damage to the lining of the intestine will cause the cells that produce the lactase and help digest the lactose to stop working resulting in temporary lactose intolerance. If the person with Celiac disease continues to eat products containing gluten the damage can become permanent and may result in permanent lactose intolerance as a secondary problem created from the primary illness.

Treatment for this type of lactose intolerance is for the person to stop consuming anything with lactose in it until the primary problem has been stabilized allowing the intestines to return to normal. Once this occurs it may only take a couple of weeks until the person can resume eating and drinking dairy products with no ill effects,