Single crystals of a complex Zintl compound with the composition Na4Ge13 were synthesized for the first time using a high-pressure/high-temperature approach. Single-crystal diffraction of synchrotron radiation revealed a hexagonal crystal structure with P6/m space group symmetry that is composed of a three-dimensional sp3 Ge framework punctuated by small and large channels along the crystallographic c axis. Na atoms are inside hexagonal prism-based Ge cages along the small channels, while the larger channels are occupied by layers of disordered sixfold Na rings, which are in turn filled by disordered [Ge4]4- tetrahedra. This compound is the same as "Na1-xGe3+z" reported previously, but the availability of single crystals allowed for more complete structural determination with a formula unit best described as Na4Ge12(Ge4)0.25. The compound is the first known example of a guest-host structure where discrete Zintl polyanions are confined inside the channels of a three-dimensional covalent framework. These features give rise to temperature-dependent disorder, as confirmed by first-principles calculations and physical properties measurements. The availability of single-crystal specimens allowed for measurement of the intrinsic low-temperature transport properties of this material and revealed its semiconductor behavior, which was corroborated by theoretical calculations.