We have developed a tomographic diffractive microscope, equipped with a fluorescence confocal scanner. We measure experimentally the lateral resolution using an edge method and by comparing tomographic images of the same samples with wide-field and laser scanning confocal microscopy images; a scanning electron microscope image serves as a reference. The experimental resolution is shown to be to about 130 nm, or lambda/(3.5 NA). This instrument also permits one to measure 3D, complex index of refraction distributions, a quantity that is not accessible to conventional microscopes, and we show how this feature may be used to observe KCl crystals, absorption of which is very weak.