Introduction: Deletions of chromosome 6q are rare. According to available statistics, there have only been 60 cases described in the world literature to date, two cases were reported in Korea. We report on a de novo interstitial 6q (q13q16.2) deletion with brain atropy and hypotonia confirmed by the microarray-based comparative genomic hybridization method. Case: A baby girl was born by vaginal delivery at 38+4 weeks\' gestation to a 27-year-old unmarried woman(gravida 2, para 1). Birth weight was 2400g (10th percentile), birth head circumference was 30cm (3rd percentile) and length was 48.4cm (50th percentile) . Apgar scores were 5 and 7 at one and five minutes. Physical examination revealed microcephaly, flat face, low set ears, cleft palate, clenched hand, abnormal parmal creases, huge umbilical hernia, both hip dislocation, progressive hypotonia. Brain MRI showed porencephaly and petechial hemorrhage at basal ganglia and thalamus, dilatation of the lateral ventricle which are consistent with brain atropy. She expired at 4 months old due to progressive respiratory weakness. The karyotypes of both parents were normal. Microarray analysis showed a single copy loss of 22 BAC clones from the long arm of chromosome 6 at 6q13q16.2. Conclusion: We describe a girl with chromosome 6q (q13q16.2) deletion associated with brain atropy and hypotonia.