Transmission electron microscopy (TEM) and focused ion beam sputtering have been used for investigations of microstructure and defect formation in AlGaAs/GaAs heterojunction bipolar transistors. The use of focused ion beam sputtering to prepare nearly ideal thin membranes within the active region of transistors for cross‐sectional electron microscopy is described. Results are obtained from as‐fabricated devices, devices annealed at temperatures of 400 °C, and devices for which ‘‘aging’’ is accelerated by operating at high‐bias conditions and heating in combination. We find that electrical operation leads to significant microstructural changes which are distinct from those observed in devices which are annealed. TEM images of the metal/semiconductor contact reveal ‘‘metal spiking’’ and facetted structures associated with alloy interpenetration. Characterization of the semiconductor heterojunctions reveal precipitates at the emitter‐base junction. Mechanisms for the formation of these defects under high‐biased operation are discussed.