Ok here goes. This is a basic summary of the research as I understand it.
Natural infection with measles, mumps and pertussis are all known to provoke temporary gut problems including increased gut permeability. Mumps and measles infection (especially close together in young children) are both known to be factors in the development of Crohn's disease and ulcerative colitis. Therefore we know these diseases affect the gut.
To understand how vaccines can affect the body we have to look at other components included in the vaccine. Vaccines contain adjuvants, some of which work as preservatives, some attenuate the virus/bacteria and some are there to provoke a response from the immune system (aluminium salts for example). Because vaccines contain attenuated forms of the disease the presence of adjuvants is neccesary in order to stimulate in the body enough of a immune response for the vaccine to have effect.
Unfortunately some of these adjuvants (particularly aliminium and thimerosol) can cause damage to the human gut (among other types of damage).
Vaccines also contain antibiotics which are known to interfere with the balance in gut flora.
So if you take the combination of; a disease which creates gut damage, adjuvants which cause gut damage, antibiotics which cause gut damage and add an ingredient which is designed to provoke an immune response (antibody creation) then you shouldn't be surprised if the end result is gut damage and antibody creation (the allergy). The development of allergies happens when food molecules pass through the damaged gut lining, and are identified by the immune system as foreign bodies, remember that this is occuring whilst the immune system is being stimulated by the adjuvant to react vigorously. The body cannot 'know' that it is only supposed to react to the vaccine and therefore reactions to harmless substances can occur.
Add to all this the immaturity of the immune system and the gut in infants plus general health, diet and an unknown number of genetic predispositions and suseptibilities. Also vaccines are injected directly into the body bypassing the mucus membranes which are a vital part of the normal, measured response of a healthy immune system in normal circumstances.
Vaccine manufacturers themselves say that an allergic disposition can be a contraindication to vaccination. Generally the vaccine schedule starts at 2 months (!!!). How many parents will be aware by this age whether their child has any allergies?
Vaccines are not tested by the manufacturers on anything other than the healthiest of children. For example low birth weight and a family history of allergy would exclude a child from being included in tests. However the vaccine is then given to all children regardless of any of these factors. Did the person who vaccinated your child ask about their birth weight? The doctor who happily injected my atopic, low birth weight child certainly did not.
Thanks anybody who has got to the end of this very long post! Long though it is, it is a very simplistic summary of huge amounts of complicated information and therefore only the most basic of outlines.
There is an increasing body of evidence (and number of vaccine damaged people) that suggests that vaccination is not all it is cracked up to be. Surely this merits serious (impartial) investigation from those who assure us that vaccines are safe.