This chapter describes the different approaches that might be taken to elucidate the genes conferring risk for obstructive sleep apnea (OSA) and for its downstream consequences. Linkage studies are useful for investigating patterns of genetic marker and phenotype co-transmission in affected families. Overall, linkage analysis has not proven, to date, to be a successful approach for discovery of sequence variants that contribute to risk of OSA or severity of the condition. Many association studies of OSA-associated traits, such as obesity, have been undertaken and several association studies of OSA have been performed. OSA is most likely very polygenetic with many gene-gene interactions given what we know already about many different risk factors. Current approaches have been largely limited to linkage studies and candidate gene association studies. Genome-wide association studies (GWAS) will likely and only lead to identifying a limited part of the heritability of OSA.