The increased prevalence of autism spectrum disorders (ASD), with associated societal and clinical impacts, calls for a broad community-based dialogue on treatment related ethical and social issues. The Stony Brook Guidelines, based on a community dialogue process with affected individuals, families and professionals, identify and discuss the following topics: treatment goals and happiness, distributive justice, managing the hopes for a cure, sibling responsibilities, intimacy and sex, diagnostic ethics, and research ethics. Our guidelines, based not on "top-down" imposition of professional expertise but rather on "bottom-up" grass roots attention to the voices of affected individuals and families speaking from experience, can inform clinical practice and are also meaningful for the wider social conversation emerging over the treatment of individuals with ASD.