The present invention relates to a computer implemented method and a system for registering and tracking an anatomical structure (1) of a patient. The method comprising the steps of: - acquiring a first stereoscopic image dataset comprising video images having different viewing angles and providing a first image content (2A) showing the anatomical structure (1)； - registering said first image dataset to a 3D image dataset showing the anatomical structure (1)； - acquiring a second stereoscopic image dataset comprising video images having different viewing angles and providing a second image content (2B) showing the anatomical structure (1), which differs from the first image content (2A)； - track the anatomical structure (1) based on the second image dataset.
