Purpose : To evaluate the role of copy number abnormalities detectable using chromosomal microarray(CMA) and diagnostic value of CMA in pediatric epilepsy patients with complex phenotypes. Methods : From January 2014 to October 2016, we retrospectively studied children with unexplained epilepsy and complex phenotypes such as developmental delay, intellectual disability, dysmorphic features, and autism spectrum disorder. The CMA was conducted with CytoScan® 750K array(Affymetrix, USA) with an average resolution of 100 kb. Results : 9 patients (male 3 and female 6 patients) with performing CMA were studied. Mean age at exam was 10.5 ± 5.0 years. All patients were taking anticonvulsant medication. Six of them were able to control their seizures with only one anticonvulsant, and the other three had seizures repeated with two or more anticonvulsants. All patients had developmental or intellectual disabilities, and 88.9% (8/9) had dysmorphic features such as facial dysmorphism and 66.7% (6/9) with clinical symptoms of autistic spectrum disorder. Total 8 copy number variants(CNVs) in 6 patients were detected. Among them, 6 CNVs were considered pathogenic (dignostic yield 66.7%). One patient occurred by uniparental disomy (15q) and 5 patients showed microdeletion; 14q11.2(57 Mb), 2q32(6.1 Mb), 1q44(4 Mb), 9p24(14 Mb), 6q26(7.6 Mb). All 2 size of benign CNVs were below 500 kb. Conclusion : The efforts to identify the various pathogenic CNVs in Korean patients furnish valuable materials to establish the cause of disease. Our data suggest that CMA is useful diagnostic tool for detecting clinically significant CNVs in children with epilepsy, especially in combination with complex phenotypes.