Adiponectin is associated with obesity and insulin resistance. To date, there has been no genome-wide association study (GWAS) of adiponectin levels in Asians. Here we present a GWAS of a cohort of Korean volunteers. A total of 4,001 subjects were genotyped by using a genome-wide marker panel in a two-stage design (979 subjects initially and 3,022 in a second stage). Another 2,304 subjects were used for follow-up replication studies with selected markers. In the discovery phase, the top SNP associated with mean log adiponectin was rs3865188 in CDH13 on chromosome 16 (p = 1.69 × 10⁻¹⁵ in the initial sample, p=6.58 × 10⁻³⁹ in the second genome-wide sample, and p=2.12 × 10⁻³² in the replication sample). The meta-analysis p value for rs3865188 in all 6,305 individuals was 2.82 × 10⁻⁸³. The association of rs3865188 with high-molecular-weight adiponectin (p = 7.36 × 10⁻⁵⁸) was even stronger in the third sample. A reporter assay that evaluated the effects of a CDH13 promoter SNP in complete linkage disequilibrium with rs3865188 revealed that the major allele increased expression 2.2-fold. This study clearly shows that genetic variants in CDH13 influence adiponectin levels in Korean adults.