Background: Although patients are increasingly involved in agenda setting within specific fields of health research, they rarely participate in decision-making on the entire breadth of health research, including biomedical research. This might be attributable to a widely held view that patients are incapable of adequate research prioritization due to a lack of relevant knowledge, a failure to look beyond their own individual problems or an inability to objectively consider long-term targets. Aims: By conducting transparent and structured consultations with asthma and chronic obstructive pulmonary disease (COPD) patients regarding their health research priorities, we aim to assess the ability of patients to prioritize research in a well-argued way. Methods: Patients were consulted through seven focus groups, a feedback meeting, and a questionnaire. The focus groups and the feedback meeting aimed to explore the entire breadth of patients' problems experienced in relation to their diseases, while the questionnaire aimed to investigate patients' prioritization of possible research targets focused on solving these problems. Results: The focus groups produced a wide range of problems, including those related to health-care organization, social environment, therapy and costs. In terms of research prioritization, patients focused primarily on biomedical issues, particularly aetiology, comorbidity and effective medication. Conclusions: The consultation procedure successfully elicited patients' research priorities including the underlying arguments. Our results indicate that asthma and COPD patients are capable of research prioritization in a well-argued way and that they highly value biomedical research. Furthermore, as they prioritized some research topics that are not covered by current Dutch research programmes, we argue that patient participation can broaden research agenda setting.