Effect of Pd addition on crystal structures of two nickel silicides, NiSi and $NiSi_2$, is investigated by using an ab initio calculation. A Pd atom substitutes a Ni and Si site, respectively, to evaluate the preferable site between them. Pd prefers Ni site to Si site in NiSi, while it prefers Si site to Ni site in $NiSi_2$. The calculated total energy also indicates that the Pd substitution to Si site stabilizes the $NiSi_2$ structure. This calculated data matches well with the experimental data obtained from Atom probe.