Abstract Study Objectives To identify genetic susceptibility variants in pediatric obstructive sleep apnea in European American and African American children. Methods A phenotyping algorithm using electronic medical records was developed to recruit cases with OSA and control subjects from the Center for Applied Genomics at Children’s Hospital of Philadelphia (CHOP). Genome-wide association studies (GWAS) were performed in pediatric OSA cases and control subjects with European American (EA) and African American (AA) ancestry followed by meta-analysis and sex stratification. Results The algorithm accrued 1486 subjects (46.3% European American, 53.7% African American). We identified genomic loci at 1p36.22 and 15q26.1 that associated with OSA risk in EA and AA, respectively. We also revealed a shared risk locus at 18p11.32 (rs114124196, p = 1.72 × 10-8) across EA and AA populations. Additionally, association at 1q43 (rs12754698) and 2p25.1 (rs72775219) was identified in the male-only analysis of EA children with OSA, while association at 8q21.11 (rs6472959), 11q24.3 (rs4370952) and 15q21.1 (rs149936782) was detected in the female-only analysis of EA children and association at 18p11.23 (rs9964029) was identified in the female-only analysis of African-American children. Moreover, the 18p11.32 locus was replicated in an EA cohort (rs114124196, p = 8.8 × 10-3). Conclusions We report the first GWAS for pediatric OSA in European Americans and African Americans. Our results provide novel insights to the genetic underpins of pediatric OSA.