During the second and third trimester of pregnancy, the outer layer of the embryo's brain, the cortex, assembles itself into six distinct layers. But in autism, according to new research, this organization goes awry—marring parts of the brain associated with the abilities often impaired in the disorder, such as social skills and language development.

Eric Courchesne, director of the Autism Center of Excellence at the University of California, San Diego, and his colleagues uncovered this developmental misstep in a small study that compared 11 brains of children with autism who died at ages two through 15 with 11 brains of kids who died without the diagnosis. The study employed a sophisticated genetic technique that looked for signatures of the activity of 25 genes in brain slices taken from the front of the brain—an area called the prefrontal cortex—as well as from the occipital cortex at the back of the brain and the temporal cortex near the temple.

The researchers found disorganized patches, roughly a quarter of an inch across, in which gene expression indicated cells were not where they were supposed to be, amid the folds of tissue in the prefrontal cortex in 10 of 11 brains from children with autism. That part of the brain is associated with higher-order communication and social interactions. The team also found messy patches in the temporal cortices of autistic brains but no disorder at the back of the brain, which also matches typical symptom profiles. The patches appeared at seemingly random locations within the frontal and temporal cortices, which may help explain why symptoms can differ dramatically among individuals, says Rich Stoner, then at U.C. San Diego and the first author of the study, which appeared in the New England Journal of Medicine.

Courchesne's earlier research had shown that the brains of children with autism have more neurons in the prefrontal cortex as well as flawed genetic signaling in this region. The absence of markers for cells that should have formed in the second and third trimester strongly suggests a time frame for the developmental error—and for future preventive interventions.