Ultimately, all signs of lactose intolerance come down to an absence or lack of the enzyme lactase. Lactase is responsible for separating the lactose in the  small intestine into glucose and galactose so that the body can metabolize the nutrients. If this does not happen, the lactose passes undigested into the large intestine, where it is broken down by the bacteria located there. Gases and other substances that cause the known complaints are formed in this process.

Gases such as carbon dioxide and methane are produced during the bacterial decomposition process of lactose in the intestinal tract. These gases build up in the intestine and cause severe and sometimes painful flatulence.

Sufferers who try to suppress the flatulence caused by carbon dioxide and methane often make the problem even worse.If the gases cannot escape, the intestine expands, resulting in unpleasant bloating of the stomach and associated stomach ache.

As well as gases, breakdown of the lactose in the intestine generates lactic acid and various fatty acids. These substances ensure that increased amounts of water enter the intestine by osmosis. The water that builds up there liquefies the stool, resulting in occasionally severe diarrhea.