The aim of this study was to assess associations between fat pad areas at various anatomic levels and the sites of lateral wall collapse and disease severity in adult patients with obstructive sleep apnea (OSA). Forty-one patients with OSA who prospectively underwent drug-induced sleep computed tomography were included. Areas of parapharyngeal fat pads and degrees of lateral wall collapse at three representative anatomic levels (nasopharynx, oropharynx, and subglosso-supraglottis), and apnea-hypopnea index (AHI) were measured. In the subglosso-supraglottic region, the parapharyngeal fat pad area in 17 (41%) patients with complete lateral wall collapse was significantly larger than that in 24 (59%) patients without complete collapse (median, 236.0 mm2 vs 153.0 mm2; P = 0.02). In multivariate regression analysis, the parapharyngeal fat pad area at the subglosso-supraglottic level (β = 0.02; P = 0.01) and body mass index (β = 3.24; P = 0.01) were independently associated with AHI. Our preliminary results supported that parapharyngeal fat pads at the subglosso-supraglottic level may be involved in the development of lateral wall collapse and then determine the severity of OSA. Further studies are warranted to investigate the effect of reducing parapharyngeal fat pads in the treatment of OSA.