As the size, weight, and performance requirements of electronic devices grow increasingly demanding, their packaging has become more compact. As a result of thinning or removing the intermediate heat spreading layers, nonuniform heat generation from the chip-scale and component-level variations may be imposed directly on the attached microchannel heat sink. Despite the important heat transfer performance implications, the effect of uneven heating on the flow distribution in parallel microchannels undergoing boiling has been largely unexplored. In this study, a two-phase flow distribution model is used to investigate the impact of uneven heating on the flow distribution behavior of parallel microchannels undergoing boiling. Under lateral uneven heating (i.e., the channels are each heated to different levels, but the power input is uniform along the length of any given channel), it is found that the flow is significantly more maldistributed compared to the even heating condition. Specifically, the range of total flow rates over which the flow is maldistributed is broader and the maximum severity of flow maldistribution is higher. These trends are assessed as a function of the total input power, degree of uneven heating, and the extent of thermal connectedness between the channels. The model predictions are validated against experiments for a representative case of thermally isolated and coupled channels subjected to even heating and extreme lateral uneven heating conditions and show excellent agreement.