The purpose of this study was to compare the effects of lumbar stabilization exercises using balls to the effects of general lumbar stabilization exercises with respect to changes in the cross section of the multifidus (MF), weight bearing, pain, and functional disorders in patients with non-specific chronic low back pain. Twelve patients participated in either a 8 week (3 days per week) stabilization exercise program using balls and control group (n = 12). The computer tomography (CT) was used to analyze MF cross-sectional areas (CSA) and Tetrax balancing scale was used to analyze left and right weight bearing differences. Both groups had significant changes in the CSA of the MF by segment after training (p < 0.05) and the experimental group showed greater increases at the L4 (F = 9.854, p = 0.005) and L5 (F = 39. 266, p = 0.000). Both groups showed significant decreases in weight bearing, from 9.25% to 5.83% in the experimental group and from 9.33% to 4.25% in the control group (p < 0.05), but did not differ significantly between the two groups. These results suggests that stabilization exercises using ball can increases in the CSA of the MF segments, improvement in weight bearing, pain relief, and recovery from functional disorders, and the increases in the CSA of the MF of the L4 and L5 segments for patients with low back pain.