Filled skutterudites are high-performance thermoelectric materials and we show how their phonon conductivity is greatly influenced by the topology of the filler species. We predict (ab initio) the phase diagram of Ba x Co 4 Sb 12 and find several stable configurations of Ba ordering over the intrinsic voids. The phonon conductivity predicted using molecular dynamics shows a minimum in the two-phase mixture regime, dominated by significantly reduced long-range acoustic phonon transport. Binary skutterudites are compounds with the general formula MX 3 (M ¼ Co, Rh, Ir and X ¼ P, As, Sb) having a crystal structure with a bcc lattice and belonging to the space group Im3. The structure consists of a periodic array of trigonally distorted and tilted MX 6 octahedrons. The metal M at the center is octahedrally coordinated by the pnicogen X [13]. The tilt of the MX 6 octahedrons gives rise to empty spaces (icosahedral voids) that form a bodycentered sublattice. As first shown in [14], the voids are large enough and can be filled by foreign species entering as cations; however, the filler solubility limit is less than a full filling of all available voids [4,15].Binary skutterudites possess very high charge carrier mobilities and the interest in these compounds as novel TE materials for power generation followed a suggestion [16] and observation [11] that their L can be dramatically reduced upon filling the structural voids. Recent research has resulted in the TE figure of merit (ZT) of n-type skutterudites approaching the value of 1.5 at 800 K [17]. While the presence of the filler species in the skutterudite matrix seems to be essential for achieving low L and hence high ZT, whether the filler acts as a rattling local vibration mode [1][2][3][4] or plays some other important role [7,[18][19][20] remains controversial. So far the only insight into the role of ordered phases on the L of partially-filled skutterudites has been the observation in [3] that the random distribution of filler ions scatter phonons more effectively than when most voids are filled. In this letter, we address the issue of ordering of the filler species, a topic that has not yet been explored and that has a great influence on phonon scattering. To this end we examine Ba x Co 4 Sb 12 , a skutterudite with a large filling fraction limit for Ba, using theoretical and computational treatments.We begin with a determination of a temperaturecomposition phase diagram of Ba x Co 4 Sb 12 by combining ab initio calculations with the cluster expansion (CE) method and the Monte Carlo (MC) simulations. Thereafter, using equilibrium molecular dynamics (MD) simulations and the Green-Kubo fluctuation-dissipation linear response theory and L decomposition, along with the phase diagram, we predict the L of partially filled Ba x Co 4 Sb 12 as a function of concentration and temperature.A prediction of phase stability at finite temperature requires the use of statistical mechanics to account for entropic contributions to the free energy. The most important source of entr...