Family and twin studies have indicated that genetic factors have an important role in panic disorder (PD), whereas its pathogenesis has remained elusive. We conducted a genome-wide copy number variation (CNV) association study to elucidate the involvement of structural variants in the etiology of PD. The participants were 2055 genetically unrelated Japanese people (535 PD cases and 1520 controls). CNVs were detected using Genome-Wide Human SNP array 6.0, determined by Birdsuite and confirmed by PennCNV. They were classified as rare CNVs (found in o1% of the total sample) or common CNVs (found in X5%). PLINK was used to perform global burden analysis for rare CNVs and association analysis for common CNVs. The sample yielded 2039 rare CNVs and 79 common CNVs. Significant increases in the rare CNV burden in PD cases were not found. Common duplications in 16p11.2 showed Bonferroni-corrected P-values o0.05. Individuals with PD did not exhibit an increased genome-wide rare CNV burden. Common duplications were associated with PD and found in the pericentromeric region of 16p11.2, which had been reported to be rich in low copy repeats and to harbor developmental disorders, neuropsychiatric disorders and dysmorphic features. Keywords: 16p11.2; copy number variation; deletion; duplication; genome-wide association study; global burden analysis; Japanese; panic disorder INTRODUCTION Panic disorder (PD) is characterized by recurrent and unexpected panic attacks, subsequent anticipatory anxiety and phobic avoidance, with the frequent development of agoraphobia. 1 The lifetime prevalence of PD is 4.7% with female preponderance. 2 PD frequently takes a chronic course, with many remissions and relapses. 3 Genetic epidemiological researches including family and twin studies have shown that genetic as well as environmental factors have an important role in the pathogenesis of PD. First-degree relatives of proband with PD have a six-fold increased risk of developing the condition. 4 Twin studies show that about 40% of liability toward PD relates to heritable factors. 5 Although several linkage studies and many association studies on more than 350 candidate genes for PD have been concluded, the results were inconsistent, negative or not clearly replicated. 6 Copy number variations (CNVs) are quantitative structural variants; they are deletions and duplications of DNA segments ranging