Absence epilepsy (AE) develops in the somatosensory cortex in children, with a bias towards females. Previous work has shown elevation of GABA levels in epileptogenesis during seizures,1 as well as changes in expression of actin, profilin 1 and a-synuclein.2 We performed a dual study of gender differences and epileptogenesis in developing rat brains by comparing samples from two rat models of each gender for genetic absence epilepsy (GAERs, WAG/Rij) to non-epileptic control (NEC) rats using mass spectrometry-based proteomics. The GAERs (Genetic Absence Epilepsy Rats) have a deficit in Cacng2, a T-type voltage-dependent calcium channel. The WAG/Rij (Wistar Albino Glaxo from Rijswijk) rats, on the other hand, have hyperpolarized HCN channels that need higher intracellular concentrations of cAMP for activation. The study design consisted of four rats of each sex from the three rat types, studied over 5 timepoints: at weaning (3 weeks), pre-puberty (6 weeks), post-puberty (10 weeks) and young adults (16 & 24 weeks). Although both mutant rat models are known to display AE, the age of onset differs. GAERs have regular seizures from the onset of puberty at around 10 weeks while WAG/Rij rats typically begin around 16 weeks. Post-mortem samples from the somatosensory cortex were analysed with SWATH-mass spectrometry, a new type of data-independent acquisition (DIA) methodology. A generalized linear model was fitted. Independent of the AE, the data revealed large differences in the proteome of the somatosensory cortex of male rats compared to females. AE changes, on the other hand, were more restricted, with a small, specific set of proteins altered in the somatosensory cortex, independently of gender. This core set of AE proteins were differentially abundant from the earliest 3-week timepoint. Thus, proteome changes in the AE models precede seizure development. We also identified additional proteins with altered abundances specific to the two different epileptic rat models. The data show both that deep proteomic brain analysis needs to consider gender and that proteins changes in the brain can occur well before seizure onset.