Axonal degeneration has been known to occur in the optic nerve (ON) of rat glaucoma model. Recently, quantitative diffusion tensor imaging (DTI) has been developed to investigate various white matter diseases in vivo. In this study, longitudinal DTI was thus employed to study such animal model in the present study. The results showed that radial diffusivity (λ⊥) and fractional anisotropy (FA) of the glaucomatous ON (gON) was increasing and decreasing respectively with time after glaucoma induction, whereas there was no significant change in the axial diffusivity (λ //). Supported by the histological staining of the ON, such changes in the two DTI-derived parameters were attributed to the 10% decrease in the axonal density of the gON as compared to nON. It was shown for the first time that DTI can be sensitive enough to detect axonal degeneration in rat glaucoma model. DTI therefore holds promise for reliable diagnoses and assessment of the glaucoma disease in human upon careful interpretation of the DTI-derived directional diffusivities.