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Purpose It was examined whether PTZ kindling at early postnatal age influences the development of absence epilepsy and induces structural changes in brains of WAG/Rij rats. Methods 25 days old WAG/Rij’s (6 F, 7 M) were treated with a subconvulsive dose of PTZ (35 mg/kg) every other day (max. 30 injections). Seizure intensity was observed and rats were considered kindled when seizures (stage 4 and 5) occurred after three consecutive PTZ injections. Controls (6 F, 6 M WAG/Rij) received saline. MRI was performed at the age of 3 (pre-symptomatic) and 6 months (symptomatic WAG/Rij’s). T2-relaxation time was evaluated in the hippocampus, thalamus, amygdala and somatosensory, piriform, retrosplenial and entorhinal cortex. EEG was recorded at 6 months by chronically implanted frontal electrodes, mean duration and number of SWDs were evaluated. Results At 3 month, a significant increase in T2 relaxation time in the somatosensory cortex for females was observed compared to female controls, this was no longer found at 6 months. A significant increase of the duration of SWDs was found in the female kindled rats compared to the female controls. Conclusion It is suggested that an increase in T2 relaxation time in the somatosensory cortex in the pre-symptomatic period can serve as a biomarker of the aggravation of absence epilepsy in female rats at a later age. It is speculated that the higher sensitivity in female kindled rats might be due to the interaction between stress induced by kindling and higher levels of glucocorticoids in female versus male rats.