A bipolar junction transistor (BJT) containing sensor that includes a vertically oriented stack of an emitter overlying a supporting substrate, a base region present directly atop the emitter and a collector atop the base region. A first extrinsic base region is in contact with a first sidewall of a vertically oriented base region. The first extrinsic base region is electrically contacted to provide the bias current of the bipolar junction transistor during sensor operation. A second extrinsic base region is in contact with a second sidewall of the base region. The second extrinsic base region includes a sensing element. A sample trench is present adjacent to the BJT having a trench sidewall provided by the sensing element.