We have investigated the structural principles and thermoelectric properties of polytypic group 14 clathrate-II frameworks using quantum chemical methods. The experimentally known cubic 3C polytype was found to be the energetically most favorable framework, but the studied hexagonal polytypes (2 H, 4 H, 6 H, 8 H, 10 H) lie energetically close to it. In the case of germanium, the energy difference between the 3C and 6H clathrate-II polytypes is ten times smaller than the difference between the experimentally known 3C-Ge (α-Ge) and 4H-Ge polytypes. The thermoelectric properties of guest-occupied clathrate-II structures were investigated for compositions Na–Rb–Ga–Ge and Ge–As–I. The clathrate-II structures show promising thermoelectric properties and the highest Seebeck coefficients and thermoelectric power factors were predicted for the 3C polytype. The structural anisotropy of the largest studied hexagonal polytypes affects their thermoelectric power factors by over a factor of two.