A study of electrical transport properties in MoSi2 thin films revealed a large resistivity difference of 57 vs 157 μΩ cm at room temperature between films formed from a codeposited Mo/Si structure and layers formed by reaction of deposited Mo with Si. The resistivity difference was found to be temperature independent. The Hall effect in the films formed from deposited Mo was a factor of four larger than in films formed from a codeposited alloy. The temperature dependencies of the Hall effect were also found to be different. Analyses of the films by Rutherford backscattering and transmission electron microscopy revealed no significant differences in thickness or grain size of the layers. The only microstructural difference is the stacking fault density, which is very high in the high‐ohmic films. The mechanism by which the stacking faults influence the electrical properties of MoSi2 and other refractory metal silicides is discussed, and relations are established between the method of deposition, the microstructure of the films, and the electrical transport properties.