What causes autism? By this I don't mean what is to blame i.e. Vaccines, Gluten or Pharmaceuticals etc.. I mean what exactly is happening in the brain to cause the autistic behaviors such as little to no communication skills, regression of skills around age 3, hand flapping etc.. I see a lot of research looking for something to blame however I see little to no research on identifying the physical causes or links (maybe I'm not using the correct search terms).
Establishing what actually happens in autistic people is difficult because it is hard to quantify someone as being autistic or not - it is common for some people to show some signs of autistic type behaviour and some people are more extreme than others - plus the symptoms are numerous:
Our understanding of the mechanisms causing autistic behaviours does not go much beyond this. This paper is a review of the neuroanatomic associations with autism which could, at least in part, help you to identify the physical differences linked to autism.
While still not entirely clear as to what causes autism, there is a growing body of research (as jonsca said), and a model is being developed.
A suggested explanation from "Causes of Autism Spectrum Disorders", that the disorder may begin in utero, with the interaction of genes and nutrients. However,
Genes seem to certainly play a role, as in the article "Support for the homeobox transcription factor gene ENGRAILED 2 as an autism spectrum disorder susceptibility locus." (Benayed et al. 2005), the homeodomain transcription gene EN2 are associated with Autism, associated with about 40% of the people they tested.
Disorders in the serotonergic system have also been found to be a mechanism of autism, according to "Serotonin transporter genotype and neuroanatomy in autism spectrum disorders" (Raznahan et al. 2009).
I hope this goes part of the way in answering your question.