BACKGROUND: Mammographic density (MD) varies throughout a woman's life. We compared the performance of a fully automated (ImageJ-based) method to the observer-dependent Cumulus approach in the assessment of within-woman changes in MD over time. METHODS: MD was assessed in annual pre-diagnostic films (from age 40 to early 50s) from 313 breast cancer cases and 452 matched controls using Cumulus (left medio-lateral oblique (MLO) readings) and the ImageJ-based method (mean left-right MLO readings). Linear mixed models were used to compare within-woman changes in MD among controls. Associations between individual-specific MD trajectories and breast cancer were examined using conditional logistic regression. RESULTS: The age-related trajectories predicted by Cumulus and the ImageJ-based method were similar for all MD measures, except that the ImageJ-based method yielded slightly higher (by 2.54%, 95% CI 2.07%, 3.00%) estimates for percent MD. For both methods, the yearly rate of change in percent MD was twice faster after menopause than before, and higher BMI was associated with lower mean percent MD, but not associated with rate of change. Both methods yielded similar associations of individual-specific MD trajectories with breast cancer risk. CONCLUSIONS: The ImageJ-based method is a valid fully automated alternative to Cumulus for measuring within-woman changes in MD in digitized films. The Age Trial is registered as an International Standard Randomized Controlled Trial, number ISRCTN24647151.