Many children with autism spectrum disorders (ASD) experience gastrointestinal symptoms such as abdominal pain, constipation, diarrhea, and bloating that exacerbate their behavioral problems. These symptoms may be related to alterations in microbial flora in the intestine. Evidence on the effect of gut flora on children with autism is very limited; however, even in healthy humans intestinal microflora is largely unexplored. Modern culturing-independent techniques allow studying complex microbial ecosystems (microbiomes) containing at least 100 times as many genes as human genome. The most informative is technique based on gene analysis of specific RNA found in all microorganisms. This novel approach was successfully used for the analysis of colon mucosa and stool samples in healthy humans and patients with inflammatory bowel disease. However, microbiome of the upper part of gastrointestinal tract in humans has been understudied in comparison to that of the colon. The objective of our study is to evaluate the entire microbial population in the upper gastrointestinal tract of children with autism to determine if there is an overgrowth of specific populations of bacteria. These data will be correlated with questionnaires on gastrointestinal symptoms and autistic behavior. The genomic data from this study might be of interest in terms of understanding the role of upper gut microorganisms in the etiology of autism and use of therapeutic strategies to alter intestinal flora.