This paper reports the cross-plane thermal conductivity of highly ordered cubic and hexagonal templated mesoporous amorphous silica thin films synthesized by evaporation-induced self-assembly process. Cubic and hexagonal films featured spherical and cylindrical pores and average porosities of 25% and 45%, respectively. The pore diameters ranged from 3 to 18 nm and film thickness from 80 to 540 nm, while the average wall thickness varied from 3 to 12 nm. The thermal conductivity was measured at room temperature using the 3ω method. The experimental setup and the associated analysis were validated by comparing the thermal conductivity measurements with the data reported in literature for the silicon substrate and for high quality thermal oxide thin films with thicknesses ranging from 100 to 500 nm. The cross-plane thermal conductivity of the synthesized mesoporous silica thin films does not show strong dependence on pore size, wall thickness, or film thickness. This is due to the fact that heat is mainly carried by very localized nonpropagating vibrational modes. The average thermal conductivity for the cubic mesoporous silica films was 0.30±0.02 W / m K , while it was 0.20±0.01 W / m K for the hexagonal films. This corresponds to reductions of 79% and 86% from bulk fused silica at room temperature.