Ion implantation is a versatile technique by which compound semiconductor nanocrystals may be synthesized in a wide variety of host materials. The component elements that form the compound of interest are implanted sequentially into the host, and nanocrystalline precipitates then form during thermal annealing. Using this technique, we have synthesized compound semiconductor nanocrystal precipitates of ZnS, CdS, PbS, and CdSe in a fused silica matrix. The resulting microstructures and size distributions were investigated by cross-sectional transmission electron microscopy. Several unusual microstructures were observed, including a band of relatively large nanocrystals at the end of the implant profile for ZnS and CdSe, polycrystalline agglomerates of a new phase such as γ-Zn 2SiO4, and the formation of central voids inside CdS nanocrystals. While each of these microstructures is of fundamental interest, such structures are generally not desirable for potential device applications for which a uniform, monodispersed array of nanocrystals is required. Methods were investigated by which these unusual microstructures could be eliminated.