OBJECTIVE: To assess hippocampal atrophy rates calculated from fluid registration methods. METHODS: Hippocampi were segmented on baseline and registered-repeat scans of 32 probable Alzheimer disease (AD) subjects and 55 controls. Fluid-based atrophy rates were calculated. RESULTS: In AD patients, the mean (SD) atrophy rates for manual, fluidly propagated, and Jacobian methods were 5.09 (3.59), 5.34 (3.43), and 3.55 (2.70) (percentage per year). In controls, atrophy rates were 1.31 (2.00), 0.89 (0.75), and 0.56 (1.12) (percentage per year). In AD, fluid propagation and manual rates were similar in means (P = 0.55) and variances (P = 0.71). Jacobian rates were smaller in mean (P = 0.002) and variance (P = 0.026) than in manual rates. In controls, fluid-propagated rates were similar in mean to manual rates (P = 0.12), but less variable (P < 0.0001). Jacobian rates were smaller in mean (P = 0.014) and less variable (P < 0.0001) than in manual rates. Both fluid methods were superior to manual measures in separating AD from controls (P < 0.0001). CONCLUSIONS: Fluid-based methods may be useful in large serial hippocampal studies.