Fabrication methods, device structures, and design structures for a bipolar junction transistor. An intrinsic base layer is formed on a semiconductor substrate, an etch stop layer is formed on the intrinsic base layer, and an extrinsic base layer is formed on the etch stop layer. A trench is formed that penetrates through the extrinsic base layer to the etch stop layer. The trench is formed by etching the extrinsic base layer selective to the etch stop layer. The first trench is extended through the etch stop layer to the intrinsic base layer by etching the etch stop layer selective to the intrinsic base layer. After the trench is extended through the etch stop layer, an emitter is formed using the trench.