The purpose of this study was to compare asymmetric mandibular prognathism individuals with symmetric mandibular prognathism individuals using a new alternate spherical coordinate system.This study consisted of 47 computed tomographic images of patients with mandibular prognathism. The patients were classified into symmetric and asymmetric groups. Mandibular and ramal lines were analyzed using an alternate spherical coordinate system. The length as well as midsagittal and coronal inclination angle of the lines was obtained. The bilateral differences of the spherical coordinates of the facial lines were statistically analyzed in the groups.There were significant differences between the groups in bilateral difference of the length and midsagittal inclination angle of the lines (p<0.05). The bilateral difference of the length and midsagittal inclination angle of the lines has significant correlation with chin deviation (p<0.05).The new alternate spherical coordinate system was able to effectively evaluate facial lines. The bilateral difference of lengths and midsagittal inclination of the facial lines might contribute to the facial asymmetry in mandibular prognathism individuals.