The difference of secondary defect formation between high-energy B+ and Al+ implanted layers was investigated by transmission electron microscopy. At the same volume concentration of implanted ions, the density of secondary defects in the Al+ implanted layers is higher than that in the B+ implanted layers and the mean defect size in the B+ implanted layers is larger than that in the Al+ implanted layers. These secondary defects are formed by agglomeration of self-interstitials and the amount of interstitials stored in the defects roughly coincides with that of implanted ions. This correlation does not depend on the ion species. The activation energies of secondary defect formation are not significantly different for B+ and Al+ implanted layers. B+ and Al+ implanted layers have different agglomerations of interstitials, which cause the differences of defect size and density. The difference does not originate from the self-diffusion of interstitials in implanted layers but is probably due to the initial nucleation of defects. © 2002 American Institute of Physics.