We report cross-plane thermoelectric measurements of misfit layered compounds (SnSe)(TiSe) (n = 1,3,4,5), approximately 50 nm thick. Metal resistance thermometers are fabricated on the top and bottom of the (SnSe)(TiSe) material to measure the temperature difference and heat transport through the material directly. By varying the number of layers in a supercell, n, we vary the interface density while maintaining a constant global stoichiometry. The Seebeck coefficient measured across the (SnSe)(TiSe) samples was found to depend strongly on the number of layers in the supercell (n). When n decreases from 5 to 1, the cross-plane Seebeck coefficient decreases from -31 to -2.5 μV/K, while the cross-plane effective thermal conductivity decreases by a factor of 2, due to increased interfacial phonon scattering. The cross-plane Seebeck coefficients of the (SnSe)(TiSe) are very different from the in-plane Seebeck coefficients, which are higher in magnitude and less sensitive to the number of layers in a supercell, n. We believe this difference is due to the different carrier types in the n-SnSe and p-TiSe layers and the effect of tunneling on the cross-plane transport.