As a field that has emerged in recent years, from multidisciplinary roots within long-standing, traditional academic infrastructures, sleep medicine has assumed highly disparate organizational structures at each institution. Access to the creativity, talent, trainees, administration, and financial investment of one or more departments at each medical center has contributed substantially to advances in sleep and biological rhythms. At the same time, however, the variability of the support structure across institutions and the ability of specific departments to develop only the most relevant aspects of a highly multidisciplinary field has substantially limited the growth of sleep medicine. Surveys in 2009 and 2012 by a Presidential Task Force of the Sleep Research Society suggested that strong, independent, self-sufficient, and cohesive administrative structures for sleep medicine were rare, if not absent. Little progress had been made toward organizational structures envisioned in the 2006 Institute of Medicine report, Sleep Disorders and Sleep Deprivation: An Unmet Public Health Problem. This white paper, written by members of the Academic Affairs Committee and then endorsed by the Boards of Directors of both the American Academy of Sleep Medicine and the Sleep Research Society, summarizes challenges to sleep medicine that arise at academic institutions. Examples of specific challenges discussed include the absence or rarity of: sleep center responsibility for sleep faculty recruitment; recruitment packages targeted for sleep; salary equity for identical work within the same sleep center by members of different departments; better equity between academic and nonacademic salaries; reinvestment of clinical or other margins back into sleep; access by qualified individuals to academic positions regardless of original specialty training before sleep; oversight of research space and resources by sleep centers; department-blind access to trainees who stand to gain most from training in sleep medicine; coordinated training in sleep and biological rhythms during preclinical medical school curricula; and sleep graduate training programs and opportunities to attract next-generation researchers into sleep and biological rhythms. Solutions to such challenges are complex and likely to differ between medical centers that themselves often have highly disparate organizational structures. However, a white paper subsequent to this one describes key goals that could be targeted, along with potential mechanisms to help ensure financial and administrative feasibility. The outline of current challenges in this paper, and a future vision and potential solutions in the next, are designed to maximize the potential that academic sleep medicine could have during coming years to improve human health in a most fundamental manner.