A heterojunction bipolar transistor structure with self-aligned sub-lithographic extrinsic base region including a self-aligned metal-semiconductor alloy and self-aligned metal contacts made to the base is disclosed. The lateral dimension of the extrinsic base region is defined by the footprint of a sacrificial spacer, and its thickness is controlled by selective epitaxy. A self-aligned semiconductor-metal alloy and self-aligned metal contacts are made to the extrinsic base using a method compatible with conventional silicon processing.