Microchip isoelectric focusing (IEF) is becomming more popular due to its short operation time, low cost, high resolution, low reagent consumption, ease of integration with various unit operations, etc. Until recently, microchip IEF had only been simulated in one-dimension which is not sufficient to model the behavior of proteins in complex microgeometries. In this study a two-dimensional numerical model is developed to simulate ampholyte-based IEF in both straight and contraction-expansion microchannels in the range, 6.21 The results of the simulation show that most of the ampholytes initially form pairs of peaks on the anodic and cathodic edges of the channel, which then move toward the channel center. A very steep pH gradient is initially formed at each electrode and gradually spreads to the middle of the channel as focusing proceeds. The numerical results reveal different focusing efficiencies and resolution in the narrow and wide sections of the contraction-expansion channel.