Device structures, fabrication methods, and design structures for a bipolar junction transistor. A first isolation region is formed in a substrate to define a lateral boundary for an active device region and an intrinsic base layer is formed on the substrate. The intrinsic base layer has a section overlying the active device region. After the intrinsic base layer is formed, the first isolation region is partially removed adjacent to the active device region to define a trench that is coextensive with the substrate in the active device region and that is coextensive with the first isolation region. The trench is at least partially filled with a dielectric material to define a second isolation region.