We consider the linear stability of exact, temporally periodic solutions of the Euler equations of incompressible, inviscid flow in an ellipsoidal domain. The problem of linear stability is reduced, without approximation, to a hierarchy of finite-dimensional Floquet problems governing fluid-dynamical perturbations of differing spatial scales and symmetries. We study two of these Floquet problems in detail, emphasizing parameter regimes of special physical significance. One of these regimes includes periodic flows differing only slightly from steady flows. Another includes long-period flows representing the nonlinear outcome of an instability of steady flows. In both cases much of the parameter space corresponds to instability, excepting a region adjacent to the spherical configuration. In the second case, even if the ellipsoid departs only moderately from a sphere, there are filamentary regions of instability in the parameter space. We relate this and other features of our results to properties of reversible and Hamiltonian systems, and compare our results with related studies of periodic flows.