We analyse United States presidential appointee positions subject to Senate confirmation without a confirmed appointee in office. These “vacant” positions are byproducts of American constitutional design, shaped by the interplay of institutional politics. Using a novel dataset, we analyse appointee vacancies across executive branch departments and single-headed agencies from 1989 to 2013. We develop a theoretical model that uncovers the dynamics of vacancy onset and length. We then specify an empirical model and report results highlighting both position and principal–agent relations as critical to the politics of appointee vacancies. Conditional on high status positions reducing the frequency and duration of vacancies, we find important principal–agent considerations from a separation of powers perspective. Appointee positions in agencies ideologically divergent from the relevant Senate committee chair are vacant for less time than in ideologically proximal agencies. Importantly, this relationship strengthens as agency ideology diverges away from the chair and towards the chair’s party extreme.