Objective In order to compare the cognitive functions in children with newly diagnosed temporal (TLE) versus frontal lobe epilepsy (FLE) and control group which consisted of healthy children the following prospective study was performed. Material and methods 39 children with TLE 24 children with FLE and 24 healthy subject were included in study. Each child had neuropsychology assessment using age-normed and validated instruments. The applied test battery consisted of measures assessing both intelligence as well as executive and motor skills. The children were reassessed one and two years. Results In all epilepsy patients there was no evidence of anatomical brain damage. There were no differences in mean age and gender between the groups. There was no significant difference in global IQ scores between the groups. Children with FLE had significantly lower scores than the other two groups in non-verbal memory tasks, presented higher attention deficit and had slower performance speed. The TLE group performed significantly worse as compared with control group in verbal learning and performance speed with no differences in attention. The correlations between the results of test and the localization of epileptic foci were performed. In long term outcome the “frontal” group performed significantly worse than other groups. detailed analysis of cognitive impairment was performed. Conclusion The children with new onset FLE present with more severe cognitive and attention problems in course of disease compared with TLE group, however the TLE group differ significantly in some measures with control group.