In this paper, we develop an active stereo system for endoscope which requires auto-calibration, because a micro pattern projector is inserted through the instrument channel during an operation and cannot be fixed to the endoscope. For solution, a new auto-calibration technique with full 6-DOF estimation of an active stereo system without any extra devices nor extra pattern projections is proposed. In the technique, the pattern projector itself is simultaneously captured with a target scene by an endoscope camera and the silhouette of the pattern projector is used to conduct 2D-3D matching by using the knowledge of the shape of the projector. In addition, the markers which is included in the projection pattern are extracted and the distances from the closest epipolar lines are calculated as for the cost function. To enhance the robustness of the reconstruction, we also propose a simple high dynamic range (HDR) imaging system for an endoscope by alternating the input power of the pattern projector ON and OFF to blink the pattern so that exposure time will vary with beat frequency, realizing a virtual multi-exposure camera. By applying our auto calibration technique with HDR imaging system, we achieved a robust and accurate reconstruction of tissue in metric 3D under practical operation of the endoscopic system, such as reconstruction of the inside of a real stomach of a pig.