To measure the three-dimensional motion of liver tumors using cine-magnetic resonance imaging (MRI) and compare it to the liver motion assessed using fluoroscopy.Liver and liver tumor motion were investigated in the first 36 patients with primary (n = 20) and metastatic (n = 16) liver cancer accrued to our Phase I stereotactic radiotherapy study. At simulation, all patients underwent anteroposterior fluoroscopy, and the maximal diaphragm excursion in the craniocaudal (CC) direction was observed. Cine-MRI using T(2)-weighted single shot fast spin echo sequences were acquired in three orthogonal planes during free breathing through the centroid of the most dominant liver tumor. ImageJ software was used to measure the maximal motion of the tumor edges in each plane. The intra- and interobserver reproducibility was also quantified.The average CC motion of the liver at fluoroscopy was 15 mm (range, 5-41). On cine-MRI, the average CC tumor motion was 15.5 mm (range, 6.9-35.4), the anteroposterior motion was 10 mm (range, 3.7-21.6), and the mediolateral motion was 7.5 mm (range, 3.8-14.8). The fluoroscopic CC diaphragm motion did not correlate well with the MRI CC tumor motion (r = 0.25). The mean intraobserver error was <2 mm in the CC, anteroposterior, and mediolateral directions, and 90% of measurements between observers were within 3 mm.The results of our study have shown that cine-MRI can be used to directly assess liver tumor motion in three dimensions. Tumor motion did not correlate well with the diaphragm motion measured using kilovoltage fluoroscopy. The tumor motion data from cine-MRI can be used to facilitate individualized planning target volume margins to account for breathing motion.