Vaccines do not cause autism. That conclusion is about as solid as any in medicine and there have been at over 14 studies that have looked for a link between vaccinations and autism and no link has been found.

Still, a large problem with autism is that there is no smoking gun , no Howard Cosell "Right there" moment where you can say THAT is the reason for autism, like you can say rubeola is the cause of measles. People need an explanation for medical problems, and if not offered they will find one.

Over the least several years the detection of autism has been pushed back earlier and earlier.

A variety of studies using home movies have found evidence of autism as early as 6 months.

Using movement analysis, detection of autism as been as early as 4 months.

These signs of autism and related disorders occur well before the <sarcasm>too many too soon</sarcasm> vaccinations could lead to autism.

Now the onset has been pushed back even further and into the womb and the developing brain. In Patches of Disorganization in the Neocortex of Children with Autism they compared the post mortem brains of children with and without autism and they

detected discrete pathological patches of abnormal laminar cytoarchitecture and disorganization in the majority of analyzed samples of prefrontal and temporal cortexes, but not occipital cortex, obtained from the boys and girls with autism

These areas of the brain develop in the third trimester and

These patches occurred in regions mediating the functions that are disturbed in autism: social, emotional, communication, and language functions.

and that given the nature of the changes

Our data support a probable dysregulation of layer formation and layer-specific neuronal differentiation at prenatal developmental stages.

It is interesting, preliminary information, and, as they note, they can see what the problem is but do not know what caused the changes, although they put forth some potential reasons in their article. If this is indeed the 'what' of autism, there is a long way to go to get to the 'why.'

As a physician I have always been amazed at the variations in anatomy in even relatively simple structures like the a foot or a heart. Only creationists marvel at the perfection of the body. I sometimes think that an underlying assumption in the US is that we are supposed to be born perfect, with no flaws or variations. Those of us who work day to day with the consequences of variations of the body sometimes marvel that anyone gets through life alive given the shoddy equipment given many of us at birth.

The brain is infinitely more complex than any other body part. It is why the new data on the autism rates in the US do not surprise me over much.

About 1 in 6 children in the United States had a developmental disability.

and

About one in every 33 babies (about 3%) is born with a (major) birth defect.

And that does not include the minor defects. I think you are lucky indeed to have a child born with nothing abnormal. My parents were not that lucky. That there will be variations in the brain, and other organs, that are a detriment to the person born with them is sad and awful and solutions need to be found.  The solution to autism, and other developmental problems, will not be found by avoiding vaccines. That much is clear. The real solutions, like much of reality, is going to be more difficult and complicated.