Methods for fabricating bipolar junction transistors with self-aligned emitter and extrinsic base, bipolar junction transistors made by the methods, and design structures for a BiCMOS integrated circuit. The bipolar junction transistor is fabricated using a sacrificial emitter pedestal that provides a sacrificial mandrel promoting self-alignment between the emitter and the extrinsic base. The sacrificial emitter pedestal is subsequently removed to open an emitter window extending to the intrinsic base. An emitter is formed in the emitter window that lands on the intrinsic base.