The etiology of obstructive sleep apnea (OSA) is multifactorial, consisting of a complex interplay between anatomic and neuromuscular factors and an underlying genetic predisposition toward this disease. Several of the factors that have been reported to play a role in the pathogenesis of OSA can serve as intermediate phenotypes in investigations targeting genetic susceptibility to OSA. A precise underpinning of the genetic basis of OSA has been thus far difficult because it is still unknown whether or not the recognized candidate genes for OSA are directly causal to the phenotype, or whether their effects on OSA are mediated through the intermediate phenotypes of OSA. Future studies utilizing phenotypically homogenous groups such as those with childhood OSA and technological advances such as haplotype analysis in a case control design are extremely promising. Developing predictive models that incorporate genetic and phenotypic markers will enable early diagnosis and, therefore, intervention, ultimately resulting in reduction of morbidity and of the public health concerns associated with OSA in obese children.