Pd-deposited clean Si(111) and (110) substrates were examined with ultrahigh vacuum (UHV) transmission electron microscopy (TEM) and scanning tunneling microscopy (STM) that are part of the newly developed UHV-TEM/STM integrated characterization system. Deposition at room temperature (RT) onto TEM (110) samples resulted in the formation of a Pd-Si mixed layer. The layer on the Si(lll edge showed contrast typical for amorphous images while that on the high index edge showed a uniform Pd,Si layer. Annealing of the Pd-deposited substrates at 673 K resulted in the formation of the Pd,Si islands on a Pd2Si layer. The formation of a 3 X 3 structure was observed on top of the Pd,Si islands with STM. Pcf deposition to TEM substrates at 673 K resulted in the formation of Pd,Si islands. A superstructure with three times periodicity was found on the surface of the island. This structure is suggested to be Si-rich and has a sub-surface layer. After low coverage deposition at RT followed by annealing at 673 K, there was formation of peculiar surface structure on a Pd2Si layer which was different from the 3 X 3 structure.