In this paper, we present an original multiple atlases level set framework (MALSF) for automatic, accurate and robust thalamus segmentation in magnetic resonance images (MRI). The contributions of the MALSF method are twofold. First, the main technical contribution is a novel label fusion strategy in the level set framework. Label fusion is achieved by seeking an optimal level set function that minimizes energy functional with three terms: label fusion term, image based term, and regularization term. This strategy integrates shape prior, image information and the regularity of the thalamus. Second, we use propagated labels from multiple registration methods with different parameters to take full advantage of the complementary information of different registration methods. Since different registration methods and different atlases can yield complementary information, multiple registration and multiple atlases can be incorporated into the level set framework to improve the segmentation performance. Experiments have shown that the MALSF method can improve the segmentation accuracy for the thalamus. Compared to ground truth segmentation, the mean Dice metrics of our method are 0.9239 and 0.9200 for left and right thalamus.