Computer assisted navigation is a widely adopted technique in neurosurgery and orthopedics. However, it is rarely used for surgeries on abdominal organs. In this paper, we propose a novel, non-invasive method based on electromagnetic tracking to determine the pose of the kidney. As a clinical use case, we show a complete surgical navigation system for augmented reality assisted laparoscopic partial nephrectomy. Experiments were performed ex vivo on pig kidneys and the evaluation showed an excellent augmented reality alignment error of 2.1 mm ± 1.2 mm.