•Pre-embedding labeling represents one of the easiest methods for molecule detection in electron microscopy.•Both peroxidase and gold labeling protocols can be used in pre-embedding procedure.•Pre-embedding offers vast opportunities to reveal and quantify molecular components at the ultrastructural level. Labeling of specific molecules for electron microscopy provides an extremely powerful tool to investigate subcellular distribution of proteins, lipids and sugars with resolution of a few nanometers. Moreover, this technology offers a unique opportunity to see how the pattern of these molecules changes in different physiological or pathological conditions. Pre-embedding labeling evolved as one of the easiest method for molecule detection in electron microscopy. It was named “pre-embedding” because the procedure involves a labeling step before the embedding of the specimen in the resin, its subsequent sectioning and analysis of sections under the electron microscope. Here we review different strategies and technical tips of the pre-embedding procedure, the potential of this method for detection and quantification of molecular components at the ultrastructural level, and the integration of the pre-embedding approach with rapidly developing light and electron microscopy technologies.