Electrides are an unusual family of materials that feature loosely bonded electrons that occupy special interstitial sites and serve as anions. They are attracting increasing attention because of their wide range of exotic physical and chemical properties. Despite the critical role of the anionic electrons in inducing these properties, their presence has not been directly observed experimentally. Here, we visualize the columnar anionic electron density within the prototype electride Y5Si3 with sub-angstrom spatial resolution using differential phase-contrast imaging in a scanning transmission electron microscope. The data further reveal an unexpected charge variation at different anionic sites. Density functional theory simulations show that the presence of trace H impurities is the cause of this inhomogeneity. The visualization and quantification of charge inhomogeneities in crystals will serve as valuable input in future theoretical predictions and experimental analysis of exotic properties in electrides and materials beyond.