Congenital Lactase Deficiency (CLD) is an autosomal recessive condition characterised by an inability to digest lactose, the disaccharide found in milk. Affected infants begin to show the symptoms of this condition as soon as they are breast fed, provided with cow's milk or lactose containing formula. These clinical features include severe watery diarrhea, abdominal bloating, flatulence, cramping of the abdomen, and vomiting. The diarrhea is severe and leads to dehydration and electrolyte loss. If left untreated and continued on a lactose diet, severe complications ensue, including renal tubular acidosis, aminoaciduria, liver damage, and ultimately death. CLD is a rare disorder. Even among the Finnish population, where most of the patients have been reported, its incidence is estimated to be 1 in about 60,000 live births.

In neonates suspected to have CLD, a confirmation of the diagnosis can be made by assaying the activity of lactase. Treatment is relatively simple. All that needs to be done is to remove lactose from the infant's diet. Once put on a milk free diet, the infant recovers rapidly, and a normal physical and psychomotor growth can be seen. After about 6-months of age, a diet with some milk may be tolerated.

The LCT gene encodes lactase, an enzyme that catalyzes the breakdown of the disaccharide lactose into its constituent monosaccharide sugars. When mutations in the gene cause a defect in the activity of the enzyme, lactose is unable to be broken down and cannot be absorbed across the intestinal walls leading to a nutritional deficiency. LCT mutations are also responsible for the Adult Type Hypolactasia (ATH).