Small animal magnetic resonance imaging (MRI) has opened a window through which brain abnormalities can be observed over time in rodents noninvasively. We review MRI studies done during epileptogenesis triggered by status epilepticus in rat. Most of these studies have used quantitative T2, diffusion, and/or volumetric MRI. The goal has been to identify the distribution and severity of structural lesions during the epileptogenic process, that is, soon after status epilepticus, during epileptogenesis, and after the appearance of spontaneous seizures. Data obtained demonstrate that MRI can be used to associate the development of brain pathology with the evolution of clinical phenotype. MRI can also be used to select animals to preclinical studies based on the severity and/or distribution of brain damage, thus making the study population more homogeneous, for example, for assessment of novel antiepileptogenic or neuroprotective treatments. Importantly, follow-up data collected emphasize interindividual differences in the dynamics of development of abnormalities that could have remained undetected in a typical histologic analysis providing a snapshot to brain pathology. A great future challenge is to take advantage of interanimal variability in MRI in the development of surrogate markers for epilepsy or its comorbidities such as memory impairment. Understanding of molecular and cellular mechanisms underlying changes in various MRI techniques will help to better understand complex progressive pathological processes associated with epileptogenesis and epilepsy.