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Electron phase-space holes are regions of depleted electron density commonly generated during the nonlinear stage of the two-stream instability. Recently, bipolar electric field structures—a signature of electron holes —have been identified in the acceleration region of the auroral ionosphere. This paper compares the evolution of electron holes in 2-D and 3-D using massively-parallel PIC simulations. In 2-D, the holes decay after hundreds of plasma periods while emitting electrostatic whistler waves. In the 3-D simulations, electron holes also go unstable and generate whistlers but, due to physical processes not present in 2-D, energy flows out of the whistlers and into highly perpendicular lower hybrid modes. As a result of this difference, 3-D holes do not decay as far as 2-D holes. The differences between 2-D and 3-D evolution may have important implications for hole longevity and wave generation in the auroral ionosphere.