In the current study, we developed an improved method for ISH at the electron microscopic level, in which we employed pre-embedding hybridization using a BrdU labeled probe followed by post-embedding immunoglobuline gold colloid staining (IGS). Because metabolic labeling of BrdU provides an almost evenly labeled DNA probe with high labeling index, pre-embeddingly hybridized BrdU-labeled probe preserves its detectable antigenicity even after the preparation of ultrathin sections. We demonstrated precise cell identification, early stage of gene expression and alternative splicing patterns using this technique.