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Deep neural network models have been widely used for environment perception of intelligent vehicles. However, due to models’ innate probabilistic property, the lack of transparency, and sensitivity to data, perception results have inevitable uncertainties. To compensate for the weakness of probabilistic models, many pieces of research have been proposed to analyze and quantify such uncertainties. For safety-critical intelligent vehicles, the uncertainty analysis of data and models for environment perception is especially important. Uncertainty estimation can be a way to quantify the risk of environment perception. In this regard, it is essential to deliver a comprehensive survey. This work presents a comprehensive overview of uncertainty estimation in deep neural networks for environment perception of intelligent vehicles.