Perfectly crystalline solids are excellent heat conductors. Prominent counterexamples are intermetallic clathrates, guest-host systems with a high potential for thermoelectric applications due to their ultralow thermal conductivities. Our combined experimental and theoretical investigation of the lattice dynamics of a particularly simple binary representative, Ba(8)Si(46), identifies the mechanism responsible for the reduction of lattice thermal conductivity intrinsic to the perfect crystal structure. Above a critical wave vector, the purely harmonic guest-host interaction leads to a drastic transfer of spectral weight to the guest atoms, corresponding to a localization of the propagative phonons.