Although no definitive genetic mutations leading to autism susceptibility have been established, the field has many new resources to tackle this difficult problem. Numbers of families at many research sites are now large, and new collaborations among these groups will allow for collections of subjects with enough statistical power to detect relatively small gene effects. New technological advances in genotyping will allow for more fine-grained genetic analysis, and more sophisticated techniques have been developed to address the vast amounts of data acquired. Researchers have also begun to focus on intermediate phenotypes associated with autism, such as elevated serotonin, increased head circumference, social difficulties, or language impairment or delay. These phenotypes may help to stratify affected cases into more genetically homogeneous subgroups, and may also occur in their clinically unaffected relatives. The study of intermediate phenotypes may allow investigators to find common gene variants that lead to autism susceptibility. Here we discuss the major intermediate phenotypes, and give an overview of current genetic analysis techniques. © 2006 Wiley-Liss, Inc.