Purpose The aim of this study to evaluate the hippocampal, frontal and thalamic lobe functions in the early stage of the juvenile absence epilepsy (JAE) by magnetic resonance proton spectroscopy (MRS). Method Fourteen patients with juvenile absence epilepsy with typical absence seizures and 10 healthy volunteer controls were included in this study. The diagnosis of the patients was in accordance with EEG findings and seizure semiology. All patients had minimum twice EEG recordings and all had typical 3-Hz generalized spike and slow-wave discharges at least on one EEG. All patients had bilateral MRS of frontal, thalamic and hippocampal regions and NAA, NAA/Cr, NAA/Cho, NAA/Cho + Cr levels were detected. Results The mean age was 14.9 ± 2.05 and 14.5 ± 1.7 of the JAE patients and control subjects, respectively. Mean seizure onset duration were 2.3 ± 0.9 years. In patient group the frontal, thalamic and hippocampal NAA/Cr ratios were 1.65, 1.78, 1.47 in right and 1.75, 1.90, 1.42 in left, respectively. While in the control group NAA/Cr ratios were 1.64, 2.42, 1.57 in right and 1.83, 2.44, 1.47 in left, respectively. There weren't any difference in frontal and hippocampal regions, but the bilateral thalamic NAA, NAA/Cr ratios of the patients were significantly lower than control group even in early stages of the disease. Conclusion The observed reductions in NAA levels and NAA/Cr ratios of bilateral thalamic regions are consistent with epilepsy related excitoxicity as a possible underlying mechanism even in early stage of JAE. However, we believe that to generalize the results of our study a prospective multicenter study is required.