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While visual autoregressive modeling (VAR) strategies have shed light on image generation with the autoregressive models, their potential for segmentation, a task that requires precise low-level spatial perception, remains unexplored. Inspired by the multi-scale modeling of classic Mask2Former-based models, we propose Seg-VAR, a novel framework that rethinks segmentation as a conditional autoregressive mask generation problem. This is achieved by replacing the discriminative learning with the latent learning process. Specifically, our method incorporates three core components: (1) an image encoder generating latent priors from input images, (2) a spatial-aware seglat (a latent expression of segmentation mask) encoder that maps segmentation masks into discrete latent tokens using a location-sensitive color mapping to distinguish instances, and (3) a decoder reconstructing masks from these latents. A multi-stage training strategy is introduced: first learning seglat representations via image-seglat joint training, then refining latent transformations, and finally aligning image-encoder-derived latents with seglat distributions. Experiments show Seg-VAR outperforms previous discriminative and generative methods on various segmentation tasks and validation benchmarks. By framing segmentation as a sequential hierarchical prediction task, Seg-VAR opens new avenues for integrating autoregressive reasoning into spatial-aware vision systems.