We performed a prospective study to examine the influence of the patient’s position on the location of the abdominal organs, to investigate the possibility of a true lateral approach for transforaminal endoscopic lumbar discectomy. Pre-operative abdominal CT scans were taken in 20 patients who underwent endoscopic lumbar discectomy. Axial images in parallel planes of each intervertebral disc from L1 to L5 were achieved in both supine and prone positions. The most horizontal approach angles possible to avoid injury to the abdominal organs were measured. The results demonstrated that the safe approach angles were significantly less (i.e., more horizontal) in the prone than in the supine position. Obstacles to a more lateral approach were mainly the liver, the spleen and the kidneys at L1/2 (39 of 40, 97.5%) and L2/3 (28 of 40, 70.0%), and the intestines at L3/4 (33 of 40, 82.5%) and L4/5 (30 of 30, 100%). A true lateral approach from each side was possible for 30 of the 40 discs at L3/4 (75%) and 23 of the 30 discs at L4/5 (76.7%). We concluded that a more horizontal approach for transforaminal endoscopic lumbar discectomy is possible in the prone position but not in the supine. Prone abdominal CT is more helpful in determining the trajectory of the endoscope. While a true lateral approach is feasible in many patients, our study shows it is not universally applicable.