Health expert Dr. Andrew Weil writes, "Food intolerances are often highly individualized and mysterious" and are "due to physical or emotional stress or exposure to environmental toxins rather than a reaction to the foods themselves." He added that intolerance is not a true allergy. Food intolerance will not show up in allergy tests. But the negative result does not mean the food agrees with your digestive system. 

Food intolerance is more common than food allergies, and the only real way to tell if you have food intolerance is by trial and error to see which foods cause you to feel sick. When you eliminate the problematic food from your diet, symptoms should disappear. 

WebMD describes one difference between a food tolerance and a food allergy as how quickly the symptoms set in, as well as the severity of food intolerance symptoms. An allergy can be life threatening in severe cases, and the symptoms happen suddenly after consuming the problematic food. The effect is less severe for a food intolerance and after eating the problem food, the onset is more gradual. Food intolerance symptoms may appear after overeating.