An analytical color fluorescence electron microscope (ACFEM) based on a high-resolution scanning electron microscope has been developed. The ACFEM enables us not only to detect cathodoluminescence (CL), which is a weak luminescence signal under electron beam bombardments, as color images, but also to analyze CL spectra. A cryo-SEM method was introduced to prevent beam effect on biological specimens. In experiments 1 and 2, we observed adult rat retinas under different conditions: hyper- and hypovitaminosis A and light and dark adaptation, which revealed that the distribution of vitamin A ester and its change under these conditions could be detected in situ by the ACFEM. In experiment 3, postnatal development of rat retina was observed under the ACFEM up to 3 weeks after birth. The retinal pigment epithelial cells of new born rats were already functioning as vitamin A storing cells. On the other hand, vitamin A ester in the developing outer segment first appeared on the 13th postnatal day, which suggests a correlation to the development of visual function. These results show that CL analysis by the ACFEM is a simple and effective new method in the field of histo- and cytochemistry.