I found this article intriguing though *very* -- as the title says -- speculative. Here, in a nutshell, are Discover's Fall 2011 "The Brain" magazine's 5 "Surprising Ideas" of what might cause autism:

1) Mother's immune system attacks the fetus's brain -- the scientist behind this theory, Judy Van d Water of UC Davis, has shown that when mothers have certain antibodies in their immune system, they give birth to children with autism. BUT only 18% of children with autism have mothers with these antibodies, so her theory still doesn't explain 4 out of 5 cases of autism.

2) Poisons from gut bacteria interfere with brain development -- there is proof that abnormal intestinal germs can affect the brain, but whether this explains autism is still a big question.

3) Extra testosterone in the womb overamplifies typically male abilities, like being great at detial and bad at social realtionships -- Simon Baron-Cohen of the University of Cambridge, is now studying frozen samples of amniotic fluid to test this theory (if fetal testoerone correlates with autism diagnoses later in life).

4) Mitochondria, which profice power to our cells, turn sickly and starve the brain of energy -- This theory relies on the fact that "the symptoms we see in children with autism are right along the lines of what we would expect in kids with mitochondrial disease," says Richard Frye, a researcher at the University of Texas.

5) Autism genes are viral -- Antonio Perisco, a researcher in Rome, thinks that genes for autism are so hard to find because they occur at the viral level, with a virus in the sperm that infects the embryo at conception. But such an infection has to first be proven to occur and then proven to cause autism.

(Original article by Adam Hadhazy, "Unmasking Autism")