Reconstructing deformable tissues from endoscopic stereo videos is essential in many downstream surgical applications. However, existing methods suffer from slow inference speed, which greatly limits their practical use. In this paper, we introduce EndoGaussian, a real-time surgical scene reconstruction framework that builds on 3D Gaussian Splatting. Our framework represents dynamic surgical scenes as canonical Gaussians and a time-dependent deformation field, which predicts Gaussian deformations at novel timestamps. Due to the efficient Gaussian representation and parallel rendering pipeline, our framework significantly accelerates the rendering speed compared to previous methods. In addition, we design the deformation field as the combination of a lightweight encoding voxel and an extremely tiny MLP, allowing for efficient Gaussian tracking with a minor rendering burden. Furthermore, we design a holistic Gaussian initialization method to fully leverage the surface distribution prior, achieved by searching informative points from across the input image sequence. Experiments on public endoscope datasets demonstrate that our method can achieve real-time rendering speed (195 FPS real-time, 100$\times$ gain) while maintaining the state-of-the-art reconstruction quality (35.925 PSNR) and the fastest training speed (within 2 min/scene), showing significant promise for intraoperative surgery applications. Code is available at: \url{https://yifliu3.github.io/EndoGaussian/}.
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