Methylene blue and neutral red were selected for staining mast cell granules by supravital injections. A new technique was applied for embedding in paraffin and Araldite®without dislocation or loss of dye. Stabilization and electron microscopic identification of the dyes were achieved by transforming them into electron-dense precipitates using phosphomolybdic acid dissolved in a paraformaldehyde-glutaraldehyde mixture to preserve the ultra structure of the tissues. It was found that in general the intensity of the light microscopic staining correlated directly with the electron density. Closer study revealed that not all cytoplasmic granules exhibited the same strong affinity for the cationic dyes. Furthermore, differences in dye distribution were observed within the granules themselves. The difference in the staining pattern can be explained by the heterogeneous occurrence of the anionic residues. Because of its high sensitivity and relatively low toxicity, the method described here is well suited for detecting the binding sites of organic cations in tissues under supravital or vital conditions