Objective Quantitative analysis of brain responses to cognitive tasks using event related desynchronization (ERD) and event related synchronization (ERS) and correlation the results with scores of neuropsychological tests in patients with BCECTS. Methods Our study included 50 children (30 patients and 20 matched controls). Clinical assessment, Neuropsychological tests, Behavioral measures, P300 averaging and Quantitative EEG analysis were carried out for patients? and control groups, in addition to brain imaging for the patients. Alpha power ERD and ERS were measured as the percent decrease or increase in alpha power produced by target tones relative to reference intervals in six different brain regions during an auditory oddball paradigm. Results Epileptic children showed a statistically significant poorer cognitive performance in the neuropsychological and behavioral tests (verbal IQ, performance IQ, letter cancellation test and number of correct responses). Moreover, both groups showed diffuse alpha power attenuation in response to the target tones, however this alpha power ERD was significantly smaller in epileptic children compared to healthy group. No significant P300 wave latency or amplitude difference was elicited between both groups and no significant correlation between alpha ERD percentage and neuropsychological results. Conclusions Children with BCECTS have subtle cognitive dysfunction, particularly in the domains of language, memory, attention and executive functions. The smaller alpha power ERD in epileptic children may be an electrophysiological index of disruptive brain activation related to the cognitive dysfunction with BCECTS. However, alpha power ERD/ERS technique could be complementary rather than supplementary to neuropsychological testing in cognitive assessment of those children.