Sixty-six participants (33 males, 33 females) with microcephaly (MC), age range from 2 to 19 years old, were evaluated. MC was classified pathogenetically into isolated MC (IMC) and multiple MC (MMC) and classified etiologically into primary MC (PMC) and secondary MC (SMC). Both IMC and MMC were further classified. Overall prevalence of epilepsy was 40.9%. Furthermore, there was a significantly higher prevalence of epilepsy in males. Main seizure type was generalized tonic-clonic seizures. Generally, learning disability (LD) was diagnosed in 93.9% and profound LD was evident in 43.9% of participants. There was an inverse correlation between severity of epilepsy and IQ but a positive correlation between severity of epilepsy and degree of LD. Differences in the success rate between monotherapy and polytherapy or response to antiepileptic drugs were not observed. Results suggest that epilepsy may be associated with the lower cognitive ability of the participants with microcephaly. The pathogenetic classification proposed is of value in delineating the prevalence of epilepsy and LD in the different varieties of MC as compared with the etiological classification.