Carbon onions were produced in a transmission electron microscope by electron beam irradiation of amorphous carbon with Pd clusters. High-resolution electron microscopy showed Pd atoms were intercalated between the graphite onion sheets, and the structural model for the intercalation was proposed. HREM images and diffraction patterns calculated for the model agrees well with the observed ones. The present work indicates that the electron-beam irradiation to amorphous carbon with Pd clusters is an effective method for the formation of intercalated onions.