When Alex was 3 months old, we met with the now deceased Dr. Jack Warner, M.D., F.A.A.P. who was a Pediatrician and Nutritionist working with families and children with Down Syndrome all over the US and abroad.  Dr. Warner developed High Achievement Potential Capsuls (Hap Caps), a vitamin combination specifically targeted to meet the nutritional needs of individuals with Down Syndrome. 

* It is important that I note that since Dr. Warner has died recently at the age of 79, there is currently NO medical professional in his place at the Warner House.  Alex was on Hap Caps from 3 months of age to 3 years of age.  
     At 3 years old, we switched Alex from Hap Caps to Nutrivene Daytime supplement.  In addition to the Nutrivene, she gets 1 tsp of flax or fish oil a day,  has a mostly dairy free diet and a very healthy diet high in antioxidants (fresh fruits, veggies, whole grains...), low in preservatives, additives, colors, sugars, bad fats.
(well..we try....she is now 14  and pretty independent!!)

"Targeted Nutritional Intervention (TNI) is a therapeutic approach utilizing defined nutritional supplementation (vitamins, minerals, amino acids, digestive enzymes presented in ratios appropriate for Down Syndrome metabolism) specifically formulated to address the metabolic oddities most commonly seen in the Down Syndrome individual.
"Targeted Nutritional Intervention (TNI) in the Treatment of children and Adults with Down Syndrome....  Principles behind its use, treatment protocols and an expanded bibliography."    Lawrence G. Leichtman M.D., FAAP, FACMG

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There is a lot of information available on nutrition and Down Syndrome.  I will not attempt to explain the particulars about nutritional abnormalities and deficiencies in people with Down Syndrome, but will provide good links to get you started on your own search.  I do however, want to make a few points.

1.  Good nutrition is important for everyone.  It can impact your energy level, mood, immune system, strength, growth, etc.
2.  Putting additives, preservatives, colors, chemicals, excess fats and sugars into your body negatively impacts so much and makes your body work extra hard to process and detoxify. .
3.  Read labels.  Buy Juice that is really Juice...not "high fructose corn syrup."
4.  Teaching a child healthy eating sets the stage for a life of good eating habits. 
5.  Individuals with Down Syndrome tend to have a weaker immune system and get colds, infections and viruses at a greater rate and intensity than the general population.
6.  Individuals with Down Syndrome tend to have certain nutritional deficiencies.
7.  Individuals with Down Syndrome tend to have an excess of free radicals (oxidative stress)  in each body cell causing imbalances.
8.  Some individuals with Down Syndrome tend to develop symptoms of Alzheimer's Disease as early as their 30'S.  Alzheimer plaques and tangles in the brain can be helped with antioxidants.
9.  Alex was on a very low dose of antibiotics from 6-11 months old due to a "grade 1 reflux" of the bladder.  Besides that, she has had a few minor colds that turned into ear infections. (although she has not had an ear infection in several years I think due to being a good nose blower now.)  She avoided bronchitis and a stomach virus when my son had it. She has never had the flu or pneumonia.  (age 6 - throat infection)
10.  Most well-meaning pediatricians only see a few children with Down Syndrome and are not experts in treating this population.  If you are looking into nutritional supplementation, I suggest copying information for your doctor so he/she can become more knowledgeable and make more informed recommendations to help you make decisions for your child. 
Vitamin Supplements, TNI
Essential Fatty Acids / Flaxseed Oil
Two types of fatty acids are considered essential to the human diet.  Omega-3 and omega-6 fatty acids cannot be synthesized in the body and must be obtained from the diet.  Omega fatty acids support brain and eye development. Researchers link low levels of omega-3 fatty acids to attention problems and learning disabililties.  Improvements in immune function, blood pressure, cholesterol levels and constipation have also been seen with essential fatty acid (EFA) supplementation.

Flaxseed Oil (organic cold pressed in the refrigerated section) or Fish Oil (pharmaceutical grade) supplements seem to be the best sources of omega-3 and omega-6 fatty acids.
1.  Many people are unable to digest the milk sugar, lactose.  Diarrhea, bloating, gas, constipation or vomiting can result.
2.  Milk is one of the most common causes of food alergies.  Allergic reactions may be skin conditions, respiratory problems, digestive issues....  
3.  Milk encourages the body to produce mucus.  Children with Down Syndrome are already more prone to upper respiratory infections and sinus problems.
4.  Soy, almond and rice milk are alternatives to cow's milk.  There are also many other foods and beverages available to ensure adequate calcium in the diet.  

there are many protein allergens in cow's milk that cause allergic reactions. Casein and whey are the two main components. The curd that forms when milk is left to sour, is called casein. The watery part which is left after the curd is removed, is called whey.

Casein accounts for 80 percent of the protein in milk and is the most important allergen found in cheese. The harder the cheese, the more casein it contains.

Whey accounts for the other 20 percent of milk. It consists of two main allergenic proteins - alpha-lactalbumin and beta-lactaglobulin.

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* This information on nutrition is provided to document what we have done, but not to say it a "cure" or "the answer."  Please research.  Every child is different.  I do think that committing to a healthy diet is extremely important to build the immune system and help the body and mind to function optimally.