Microspheres made from optical glasses such as silica and chalcogenide are used as both passive and active optical elements in micro-optics systems and devices. The homogeneity of the microspheres is crucial to their optical quality and performance in such devices and so it is essential, in optimizing such systems, that techniques with nanometer scale resolution are developed to measure the internal structure and homogeneity of such spheres. In this work an analytical protocol based on focussed ion beam milling, combined with secondary ion and secondary electron imaging, has been developed to study the internal homogeneity of glass microspheres. The results have shown that silica microspheres with diameters of three to five microns, fabricated by a sol-gel method, have internal inhomogeneities and voids that will lead to non-uniform optical properties. The FIB milling and imaging technique developed has been found to be a very useful method of studying such inhomogeneities, which have been proposed, but never previously observed, in glass microspheres. The FIB based technique has also been used on larger chalcogenide glass (Ga 2S 3:La 2S 3) microspheres (diameter of order 70 microns) but no inhomogeneities have been observed at the spatial resolution of a few microns so far achieved for these larger microspheres. This study suggests that the FIB based milling and imaging technique may have potential for quantitative use in the measurement of morphological variations in such systems as well as in the study of aging processes in micron-sized glass spheres.