The goal is to return to a diet of simple, carefully selected, natural foods. Fresh or frozen vegetables, fruit, poultry, and fish are the basic food choices. These are staple foods that allow us to reconstruct daily menus, with confidence of good nutrition, and stable life-long eating habits. For most children, a shift to meals featuring cooked vegetables is the most important change.

The Alpha Nutrition Program includes primary foods, popular all over the world and, at the same time, excludes other foods that are staples in current North American diets. It may be that we are responding to modern problems of additives and contaminants in our food supply. It may be that we each too much of our staple foods, especially meat, wheat, eggs, and milk. Alpha Nutrition food selection is success-oriented, and has no other basis in taste, preference, or ideology. The design of the  program was originally based on experience solving the problem of delayed pattern food allergies. The first foods on the diet are chosen because of a low probability of adverse reactions. At the same time, Alpha Nutrition design emphasized foods that are nourishing and are associated with the prevention of many common food-related diseases.

The food problems that concerned us involves a complicated series of body dysfunctions. Since there is no current testing method that reliably identifies the causes food-related illnesses, we cannot specify a short list of foods to avoid, and assume that everything else will function properly. We can assume that diets with low allergenic potential will be helpful in most children, and begin therapy with a "hypoallergenic diet". When symptoms are reduced, foods may be added back in an orderly manner to determine the limits of your child's tolerances. You become the therapist and quickly learn to interpret your child's symptoms in a biological manner and make appropriate decisions about the right food supply. By monitoring your child's progress, you can identify recurring problems, and change the food selection to avoid them. If symptoms recur, you retreat to an early stage of the program, even to the initial Phase 1 foods, for several days, to allow the disturbance to clear. The strategy is to custom-fit a diet plan to each child's needs.