Experimental febrile seizures (FS) are known to promote hyperexcitability of the limbic system and increase the risk for eventual temporal lobe epilepsy (TLE). Early markers of accompanying microstructural and metabolic changes may be provided by in vivo serial MRI. FS were induced in 9-day old rats by hyperthermia. Quantitative multimodal MRI was applied 24 h and 8 weeks later, in rats with FS and age-matched controls, and comprised hippocampal volumetry and proton spectroscopy, and cerebral T2 relaxometry and diffusion tensor imaging (DTI). At 9 weeks histology was performed. Hippocampal T2 relaxation time elevations appeared to be transient. DTI abnormalities detected in the amygdala persisted up to 8 weeks. Hippocampal volumes were not affected. Histology showed increased fiber density and anisotropy in the hippocampus, and reduced neuronal surface area in the amygdala. Quantitative serial MRI is able to detect transient, and most importantly, long-term FS-induced changes that reflect microstructural alterations.