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Background: Biomedical research is influenced by many factors, including the involvement of stakeholder groups invested in research outcomes. Stakeholder involvement in research efforts raise questions of justice as their specific interests and motivations play a role in directing research resources that ultimately produce knowledge shaping how different conditions (and affected individuals) are understood and treated by society. This issue is highly relevant to child psychiatry research where diagnostic criteria and treatment strategies are often controversial. Biological similarities and stakeholder differences between attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) provide an opportunity to explore this issue by comparing research foci and stakeholder involvement in these conditions., Methods: A subset of ADHD and ASD research articles published between 1970-2010 were randomly selected from the PubMed database and coded for research focus, funding source(s), and author-reported conflicts of interest (COIs). Chi-square analyses were performed to identify differences between and within ADHD and ASD research across time., Results: The proportion of ADHD research dedicated to basic, description, and treatment research was roughly similar and remained stable over time, while ASD research showed a significant increase in basic research over the past decade. Government was the primary research funder for both conditions, but for-profit funders were a notable presence in ADHD research, while joint-funding efforts between non-profit and government funders were a notable presence in ASD research. Lastly, COIs were noted more frequently in ADHD than in ASD research., Conclusions: Our study shows significant differences in research foci and funding sources between the conditions, and identifies the specific involvement of for-profit and non-profit groups in ADHD and ASD, respectively. Our findings highlight the relationship between stakeholders outside the research community and research trajectories and suggest that examinations of these relationships must be included in broader considerations of biomedical research ethics.