Ligand-stabilized palladium amorphous nanoparticles with various monodispersed sizes ranging from 2 to 6 nm were synthesized and compared with palladium crystalline nanoparticles. The nanoparticles were characterized by high-resolution electron microscopy (HREM), X-ray photoelectron spectroscopy, and scanning tunneling microscopy/spectroscopy (STM/STS). Both HREM images and electron diffraction patterns show quite clear differences in structures between crystalline and amorphous palladium nanoparticles. STS spectra exhibit fine structures in addition to the Coulomb blockade and the Coulomb staircases in the current-voltage (I-V) curves for the crystalline Pd nanoparticles when the diameters are smaller than 4 nm but only pure effect of Coulomb blockade and Coulomb staircases for amorphous Pd nanoparticles, which further indicates the differences in electronic structures.