PURPOSE: To determine the issues important to stakeholders in today's academic surgery departments, to query key stakeholders about possible solutions, and to investigate the correlation of organizational alignment among department stakeholders with department performance. METHOD: Between July 2003 and October 2005, the author designed, piloted and carried out a study in which he interviewed key stakeholders-deans, chief executive officers/chief financial officers (CEOs/CFOs) of hospitals and health system practice plans, surgery department chairs, and surgery department members-from 12 randomly selected academic surgery departments. Important issues and solutions were identified and comparisons among stakeholder groups performed. Alignment was evaluated both among and within groups and organizations. RESULTS: Stakeholders (11 deans, 9 CEO/CFOs, 12 department chairs, 10 department faculty members) identified 12 issues and offered potential solutions and responses important to today's academic surgery department. One issue identified was promotion and tenure; nearly all stakeholders stated that its current form needed to be changed. Alignment analysis was incomplete because of inconsistent outcomes reporting. CONCLUSIONS: The uniformity of issues facing academic surgery departments and the similarity of the solutions proposed to address these issues (both study findings) suggest a need to change the paradigm and think "outside the box." The study findings suggest that academic surgery departments, under strong leaders, must establish a unified culture, define a compelling vision, articulate a clear mission, and develop fully accepted values to be successful. The study findings could be useful in designing and developing academic surgery departments in today's health care environment.