Background: General practitioners (GPs) are increasing involved in the care of children with autism spectrum disorders (ASDs), and prescribe and/or manage psychotropic medications for these children. Few published reports of perceptions of GPs regarding use of these medications exist in the literature. Objective: Qualitative analysis of comments by 177 GPs regarding psychopharmacology use in children with ASDs. Methods: A postal questionnaire survey containing both close- and open-ended questions was conducted in New South Wales, Australia. Results: Respondent GPs were more likely to be females graduated from Australian medical schools and reported an interest either in child or in mental health. The respondents demonstrated good understanding of the issues surrounding psychopharmacology use in children with ASD based on contemporary literature on this topic. The main themes included concerns regarding medication safety, evidence for their use, and role of these medications as an adjuvant to behavior management. GPs reported a lack of experience of these medications, and would often prescribe only under the supervision of specialists. GPs with greater confidence and involvement with children of ASDs prescribed more medications; whereas GP reporting more concerns with regard to medications prescribed less. Conclusion: Respondent GPs have good understanding of psychotropic medications but need support from specialists for managing these medications in children with ASDs. Future larger studies should explore the utility of collaborative models of care for GPs to work in close partnerships with specialists.