The academic health sector will face major changes in governance, health care delivery, educational requirements and research programs over the next decade. Increased emphasis on disease prevention and health outcomes, the need for evidence to support both clinical and policy decisions, educational changes both in content and delivery, and the importance of working in teams will challenge the academic health care community. Large research teams may require new ways of training and nurturing young investigators, including improved grant writing and knowledge translation, human resource management skills and the ability to interact with disciplines that have different research methodologies. MD/PhD and Clinician Investigator Programs may help to fill these gaps in medicine, but nursing is faced with a serious shortage of doctoral-trained educators and researchers and may need targeted programs to achieve a critical mass of academics able to accept leadership roles. The success of the Quebec model of support for health research networks and researchers is encouraging. There is a leadership gap within health care institutions that spans jurisdictions and affects both institutional performance and individual careers. Young investigators need good mentors and adequate protected time to acquire the skills necessary for leadership roles. Policy changes within health care institutions and academic organizations will be necessary to adapt to the coming decade. The Canadian Institute of Academic Medicine is committed to developing better mentoring strategies for the next generation of academic leaders and to creating formal assessments of major Canadian health issues that can be used by health care advocacy groups when talking with policy-makers.