A food intolerance is the body’s inability to digest a certain food, thus causing a reaction (I.e. lactose intolerance). The immune system is not usually involved in a food intolerance. Every food molecule requires an enzyme to help digest it (carbohydrates=amylase; protein=protease; lactose=lactase). When a person consumes a food that they do not produce enough enzymes to digest, an intolerance to that food may develop, which can then cause digestive disturbances and other underlying health issues.
For example, people who are lactose intolerant are usually deficient in the enzyme lactase, which is responsible for breaking down lactose (milk sugar) in milk. Another intolerance that is increasing in popularity is gluten intolerance, which is related to the consumption of wheat and other gluten-containing grains.