Background: Epilepsy is one of the most common neurological disorders in humans with prevalence of 1% and lifetime incidence of 3%. Several chromosomal abnormalities have been described that may cause epilepsy and intractable epilepsy syndromes but the role of many copy number variants (CNV) is unknown.

Microarray-based genomic copy-number analysis (chromosomal microarray - CMA) gives a chance to detect very small chromosomal imbalances associated with different diseases. Our aim was to find out the frequency of using CMA in newly diagnosed epilepsy in common clinical practice in Southern Estonia.

Methods: the study group included all newly diagnosed children with epilepsy from 2009-2011 in Southern Estonia. All the preformed CMA-s as common clinical practice and other investigations were recorded in addition to general characteristics of the patients.

Results: From 122 children with newly diagnosed epilepsy CMA was preformed in 15 (12.3%). From these 15 children 11 were boys (73.3%). 20% (3) of CMA had some changes, and 2 (66.6%) had mutations that can be related to epilepsy. One patient had 8p23 syndrome (intellectual disability, dysmorphic features and epilepsy), the other had microdeletion on 22q13.2 that consists the MCHR1 gene.

Intractable epilepsy or epileptic encephalopathy developed in 17 (13.9%) of 122 newly diagnosed epilepsy patients. As a first line diagnostic investigation CMA was preformed in 8 (53,3%) of 17 children.

Conclusion: CMA is a useful diagnostic tool in detection of CNV's in epilepsy and it should be part of common clinical practice.