The infantile epileptic encephalopathies are a heterogeneous group of disorders where in about 30% of cases the cause remains unknown. Chromosomal aberrations, identified by karyotype analysis, constitute one of the major causes for these disorders. The new molecular cytogenetic techniques such as fluorescence in situ hybridization, multiplex ligation-dependent probe amplification (MLPA) and single nucleotide polymorphism array analyses may allow us to discover additional submicroscopic chromosomal rearrangements in this group of patients. Herein, we describe a girl with infantile epileptic encephalopathy. Fluorescence in situ hybridization, MLPA and single nucleotide polymorphism array analyses revealed a microdeletion and microduplication at the 1p36 region. Because of that, we further screened a cohort of 38 patients with infantile epileptic encephalopathy by using MLPA analysis to exclude the presence of subtelomeric microdeletions or microduplications. One patient was shown to harbor a microduplication at 11q25, which is however most likely a benign copy number variant derived from the healthy mother. No disease-causing dose changes were identified, indicating that unbalanced rearrangements at the subtelomeric regions may not be a common cause for infantile epileptic encephalopathy. However, when the patient has infantile epileptic encephalopathy and other features such as dysmorphic facies or major congenital anomalies, molecular cytogenetic analysis is warranted.