<b>Background:</b> Obstructive sleep apnea (OSA) is a risk factor for cardiovascular disease (CVD), but the genes involved in this relationship have not been elucidated. <b>Objective:</b> To Identify genetic variants associated with several phenotypes of OSA. <b>Methods:</b> The sample included 198 males and 140 females who were assessed for OSA by polysomnography. Individuals were categorized in cases (with OSA; Apnea hypopnea index: AHI ≥ 5) and controls (with no-OSA). Genomic DNA was isolated from saliva and genome-wide association SNP array assay was performed. In a secondary analysis the SNP with the highest significance was analysed in 400 additional individuals (200 with OSA and 200 with no-OSA). Clinical phenotypes and comorbidities were documented. Multivariate analysis, Benjamini-Hochberg (B-H) procedure and odd ratio tests were performed. <b>Results:</b> GWAS data analysis revealed risk variants at the NT5C3B (exm2253003, p=2.54E-06; OR= 2.116) and KLHL11 (rs9303319, p=8.75E-06; OR=2.078) genes. NT5C3B demonstrated the greatest statistical significance, and has previously been associated with airflow limitation in smaller airways. Therefore, exm2253003 was analysed in the second part of the study and showed statistically significant difference associated with the risk for OSA (p=0.049 OR=2.22 CI:1.011-4.88). In the group of individuals with OSA and the NT5C3B variant, 88.33% of individuals had coronary artery disease, 66.7% had arterial hypertension and 26.2% had atrial fibrillation. There was no correlation between severity of sleep apnea (AHI ≥ 30) and the presence of comorbidities. <b>Conclusions:</b> These findings suggest that the risk to develop OSA and CVD are mediated by genetic variants.