Purpose. We investigated changes in anisometropia and aniso-axial length with myopia progression in the Correction of Myopia Evaluation Trial (COMET) cohort. Methods. Of 469 myopic children, 6 to <12 years old, enrolled in COMET, 358 were followed for 13 years. Cycloplegic autorefraction and axial length (AL) in each eye were measured annually. The COMET eligibility required anisometropia (interocular difference in spherical equivalent refraction) of ≤ 1.00 diopter (D). For each child, a linear regression line was fit to anisometropia data by visit, and the regression slope b was used as the rate of change. Logistic regression was applied to identify factors for significant changes in anisometropia (b ≥ 0.05 D/y, or a cumulative increase in anisometropia ≥0.50 D over 10 years). Similar analyses were applied to aniso-AL. Results. A total of 358/469 (76.3%) children had refractions at baseline and the 13-year visit. The mean (SD) amount of anisometropia increased from 0.24 D (0.22 D) at baseline to 0.49 D (0.46 D) at the 13-year visit. A total of 319/358 (89.1%) had slopes jbj < 0.05 D/y and 39 (10.9%) had slopes jbj ≥ 0.05 D/y, with only one negative slope. Similarly, 334/358 (93.3%) children had little change in aniso-AL over time. The correlation between changes in anisometropia and aniso-AL over 13 years was 0.39 (P < 0.001). The correlation between changes in anisometropia and myopia progression was significant (r =-0.36, P < 0.001). No correlation was found between baseline anisometropia and myopia progression (r=-0.02, P =0.68). Conclusions. Myopia and axial length progressed at a similar rate in both eyes for most children in COMET during the period of fast progression and eventual stabilization. These results may be more generalizable to school-aged myopic children with limited anisometropia at baseline. (ClinicalTrials.gov number, NCT00000113.). © 2014 The Association for Research in Vision and Ophthalmology, Inc.