1.- Elimination and reintroduction diet
It consists of eliminating a certain food for a while and seeing if symptoms resolve. Then we reintroduce the food and we check if symptoms improve. If that is the case, it is certain that this kind of food is harmful.
The problem with this approach is that you need to have enough willpower to eliminate a certain food, especially considering that the food you have intolerance to can also create a dependency with the consequent withdrawal symptoms when they are avoided.
The necessary time of exclusion of a food before you start noticing results depends on the type of disease. For allergies and digestive disorders the time is usually quite short, for example one week, but in the case of chronic inflammatory diseases a trial period of about three months is often required, while in the case of neurological diseases it may even be six months.

This type of test is particularly suitable for small children and babies, this way we can avoid having to inject them.
Similarly, in the reintroduction phase it can occur that no symptoms are present at first, but after a few months of consuming the food again the symptoms reappear. This happens because the antibodies decline during the elimination phase, and then gradually increase during the reintroduction. As a consequence, until you reach a sufficient amount to notice the symptoms again, the intolerance goes unnoticed.
So ideally, you should embark on an elimination/reintroduction diet with one food at a time, and with a period of about three months on average for each. That is, eliminating a food during three months, plus three months’ reintroduction time of the same. Then, the same process can be done with a different food. As you can imagine, this process is often not feasible. 
As mentioned, the reaction with the introduction of a food may take some time (weeks or months) to begin to manifest after a clearance time, but when it does, the reaction occurs shortly after ingestion, usually from a few hours to maximum two days’ time. However, the effects of a food may take several days to manifest. For example, the time from ingestion of sugar to the development of intestinal worms usually takes about five to seven days.
The guidelines I would recommend to follow during the reintroduction phase are as follows:

1.- Start the reintroduction very slowly, with small amounts of food, for example, a teaspoon.

2.- Wait two days to see if there is any reaction. If there is no reaction, then gradually increase the quantity of food and wait two more days.

3.- When you have reached a normal amount of food, and there has not yet been any reaction, continue eating it but only once or twice a week. Take this precaution for at least three months.

4.- At this stage, you can reintroduce another food in the same way.

5.- Avoid taking two suspected foods which can create reaction on the same day, leave a two-day gap between two suspected foods. This way, you can reintroduce up to three different foods in three months.

6.- If there is a reaction, identify which suspected food was the last to be eaten. Return to eliminate that food to check.

7.-  After three months of reintroduction of a food without problems, you can increase the frequency of consuming it if desired. In any case, continue checking, during a time, one month for example, if there is no reaction when increasing frequency.

8.- Once you are sure that the food is tolerated without any problem, you can move on to introduce a different food.
It may also be useful to write a diary noting down everything you eat every day as well as your health status.
For each person a different pace could be recommended: at the elimination phase, for some people it is best to start eliminating all suspected foods at once from the beginning, in other cases it is better to go slowly eliminating the suspected foods one by one. The reintroduction phase may go faster in some cases, especially when the amount of food that had to be removed is reduced and diseases that trigger are mild, and in other cases it is better to go slower, especially when associated diseases are serious and there are several intolerances.

2.- Provocation diet
This diet is about increasing the amount of suspect food taken very slowly and at the same time observing if the symptoms improve.
It might be dangerous in the case of certain acute diseases. But it may be the only option if you are not able to remove foods from your diet in order to do the elimination/reintroduction test.

3.- Analysis of medical intolerances
There are several food intolerance analyses: blood antibody test for immune intolerances; respiratory analysis for sugars such as lactose, sucrose and fructose; stool sample analysis for the imbalance of intestinal flora; urine test for opioid peptides from gluten and casein, etc. To learn more, please read this page.
The disadvantage is that you usually do not find all intolerances, due to the fact that science is not advanced enough. These intolerances that can not be found with analyses are called "food sensitivities". It is known that there is some kind of intolerance because the person feels better when avoiding a specific food, but there is no reaction to any analysis (neither immune, nor bacteriological, nor enzyme reaction).
In most cases the analyses usually find major intolerances, but then, it is you who must continue to investigate the details of what your diet should be like.

4.- Energetic therapies
There are many energy therapies to detect energy blocks to different foods: kinesiology, NAET method, bioresonance, etc. Methods are time-consuming, since few food is tested in each session. Usually there are some intolerances found, but I believe that medical tests are more accurate, reliable and faster as well. In contrast, during the same session, a treatment is done to try to heal this energy blockage. Before trying it, I advise you to speak with someone who has followed the treatment. Personally, my doubt is whether this is a natural method which, like conventional medicine, only "turns off" alarm signals that the body sends in order to indicate a problem, while the real cause of the problem still remains there.
The advantage is that it is noninvasive, so it can be interesting in the case of children.
 

Issues to consider when going on an elimination/reintroduction diet

1.- Bowel transit time
Bowel transit time from ingestion of food until it reaches the anus, may differ greatly depending on the type of food and how fast or slow the bowel transit of the person is. It takes much longer to digest meat than carbohydrates, and it takes longer to digest carbohydrates than fruit and vegetables. Normally for a meal containing vegetables, carbohydrates and proteins it takes between 12 and 24 hours to be fully digested, but for some people, especially women, it may take up to 48 hours. So the reaction to food may take more than two days to produce.
But the effects of a food may take several more days to show. For example, the time from ingestion of sugar to the development of intestinal worms usually takes about five to seven days.

2. – Intolerance to certain substances
Food intolerance can be caused by substances that can be found in different kinds of food, for example, histamine can be found in fish, pork, some fruit and vegetables, all fermented products (such as meat, vegetables, milk, etc.), chocolate, seafood, etc.
Another example could be when due to a yeast infection there is intolerance to all carbohydrates and sugars present in milk products, cereals, legumes, fruits and nuts. 
In other cases, intolerance is as specific as to a certain range of a food, for example, only to red potatoes or green beans. 
You could also be intolerant to the way food is prepared, for example, fried, or to the oil used for cooking or dressing.
Similarly, there may be an allergy to any of the materials used in the kitchen or for the packaging of food. For example you could be hypersensitive to aluminum, which is one of the adjuvants in vaccines, or mercury, the most toxic heavy metal, which is present in big oily fish, in vaccines, amalgams, broken thermometers, some industries, etc.

Regarding toxins, fortunately the body has the ability to remove them. However, due to certain circumstances, for some people it is more difficult to eliminate toxins or they can develop a hypersensitivity to certain products, especially when the exposure is chronic. It is really difficult to identify this type of poisoning. We can even be talking about an electromagnetic hypersensitivity.
There are also some analyses to determine intoxication or hypersensitivity to a substance, but thereafter, finding the source is a very difficult task, since we are surrounded by heavy metals. Read this article to know more. Sometimes there is only one solution: to go and live in a cabin in the country, raising our own cows and growing our own vegetables!

3.- Quantity, frequency and combination
The intensity of the diseases caused by some intolerances often depend on the amount and frequency of food eaten during the week. Also, it's better avoiding eating proteins and carbohydrates in the same meal to improve digestion, and fruits must be eaten alone, as snack for example.

4.- Food addictions and intolerances
Normally, our bodies develop an addiction to foods which we are intolerant to. When you start the  elimination diet of the food you are intolerant to, you may undergo a period of feeling worse at first, which may last from a few weeks to months, depending on the person. This is known as withdrawal syndrome and extinction syndrome. These syndromes are explained by several theories:
4.1. Some of the foods which we are intolerant to, mainly gluten and casein produce dependence due to the fact that they produce opioid peptides that act like morphine or opium.
4.2. Intolerance leads to swelling, which counteracts the intrinsic production of endorphins, which are substances that cause well-being. When the inflammation no longer exists, there is no production of endorphins and so no sense of well-being.
4.3. By avoiding intolerant foods that were feeding undesirable gut bacteria we manage to kill these bacteria. They starve to death and by dying they release large amounts of toxins, which cause symptoms to worsen. This is the the die-off reaction.
4.4. Undesirable bacteria that live on intolerant food send signals to the brain so that the person continues eating those foods that nourish the bacteria. 
As a general rule, food that is not intolerant produces no significant effect on health when removed. For example, when we no longer eat some fruit or vegetables because their season ends, we do not feel any improvement or worsening. Instead, most people experience a major impact on health shortly after removing cereals that contain gluten, dairy products, sugar, coffee, chocolate, etc. from their diet.

5.- Eliminating addictions and intolerances
Eliminating food addictions and intolerances is very difficult. Habitually, when food is removed from a child’s diet, which he/she is addicted to, then he/she begins to like most other food, which makes it easier for the parents. Children often just want to eat carbohydrates, sugars and dairy products, which are the most addictive kinds of food. When these products are removed, children begin to accept vegetables, fruit, meat, fish, eggs, etc.

The techniques that can be used to eliminate an addiction are numerous. In the case of children simple parental authority is sufficient, it only requires courage from the part of the parents. In the case of adults it is more complex, usually support of family members is needed, and other kinds of support can be of use as well, such as psychotherapeutic therapies, hypnosis, NLP (neuro-linguistic programming), etc.

6.- Hidden food intolerance
Some intolerances may hide others. For example, cereal intolerance often results in intolerance to other foodstuffs, such as good fats.This is due to the fact that microbial growth resulting from excess carbohydrates also inhibits proper liver function and causes a deficiency in lipid digestion. So, many people think they have an intolerance to fats and oils, while in fact the cause may be an intolerance to cereals. 
Many times a certain food does not make you feel well and the cause is not the food itself but other circumstances that cause a greater sensitivity to that food. Factors that influence this can be quite varied: stress, fatigue, other food intolerances, but also the way food is prepared, as well as the quality of food, or the oil, fat or sauce that is used, etc.
Most of my patients complain that when avoiding gluten they begin to have more gastro-intestinal problems, while other health problems such as pain, allergies, infections, etc. decrease significantly. The exact reason is unknown, however, probably what happens is that by eliminating gluten the body "wakes up", stops being "drugged" and notices much easier when other foods are harmful. For example, fruit may start causing digestive problems with bloating and gas, while previously there were no similar problems. Surely there has been a fructose intolerance previously as well, the person just did not realize.

7.- From major to minor intolerances
It may take several years to make a list of intolerant foods. It starts with the great families: gluten, dairy, nuts, eggs,... and afterwards we may find more little details, such as apple and pear, red cabbage, etc.

Changing daily routines can help find intolerances. You can take advantage of weekends, holiday periods or trips to see if the symptoms change in intensity, if they increase or decrease. It may give you a hint about the cause or origin of disease to which you are exposed to day by day, as it  changes while on holidays.

8.- The progress of intolerances
Once intolerances are identified, they can evolve over time, especially if problems of the bowel are not resolved. This is what usually happens when replacing for example gluten for other gluten-free cereals. The possible cause is a celiac disease when eating gluten-free grains like corn or rice. After consuming these cereals for some time an intolerance to these may appear as well. The explanation for this occurrence is that intolerances, especially immune ones appear due to the leaky gut syndrome. This is the condition in which the gut is "leaky" and lets partially digested proteins through, which are identified as invaders and activate the body's defenses. Consequently, we can become intolerant to more and more foods over time. So it is necessary to overcome the leaky gut syndrome to end intolerances, taking certain therapeutic foods such as lacto-fermented foods, meat and fish broths, vegetable juices and fruit, and perhaps some supplements like probiotics and essential fatty acids.

9.- Food intolerance in children
If a child is sick, there is a double problem. On one hand having to inject a child in order to do intolerance analyses is not a pleasant experience. On the other hand, children are exceptionally resistent to changes in their diet and especially in the case of an addiction (such as to sugar, carbohydrates, sodas, etc.) which is quite a common occurrence in their case. Parents would like to know in advance which diet is best for their child, to be sure that such a difficult process as the change of the diet will be worth it. Unfortunately, nutrition science is not advanced enough so that the therapist-nutritionist can confidently predict the success of a diet. However, there are certain diets that usually work for most diseases that children may have, supported by hundreds of successful cases, such as the GAPS diet in the case of psychological and neurological conditions. These are always worth a try.
Sometimes we are blinded eating a certain food because we believe it is very beneficial to health, such as the myth of drinking a lot of milk is good for us to get plenty of calcium. On the contrary, if there is a milk intolerance, the development of undesirable bacteria causes that calcium can not be absorbed, and conversely, the milk is feeding these bacteria. In this way, we force children to take certain foods because we believe those are beneficial to health, regardless of the possibility that it can be rejected because they have an intolerance. For example, when children reject certain fruits, vegetables, or dairy products, etc. Rejection may also be due to an addiction to other products such as gluten and milk. In those cases we must investigate which of the two possibilities is true.