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Most solutions to food intolerance issues come to down to modifying the diet.

First, is to identify the foods or food chemicals that are causing the symptoms.  This is generally done through an elimination or detection diet.  Through this process you will be able to find the items that are causing the symptoms.  Over time you may be able to re-introduce certain foods and tolerate them to a degree.

With some problems such as Candida, an anti-fungal medication is recommended in conjunction with a no/low yeast diet.   The medication gets the Candida under control and the diet helps it from recurring.  The process of eliminating Candida is often much longer as the symptoms are being caused by an organism rather than simply a reaction to a food or food chemical.

The Royal Prince Alfred Hospital Allergy Unit in Sydney has developed a straightforward approach to an elimination diet which we followed when we determined that our son was likely to be suffering from food intolerance.  Their site also has useful information about food intolerance generally.

We took a similar approach with our son when he was 1 1/2.   The details are here