The association between sleep apnea (SA) and peripheral artery disease (PAD) remains debatable, and there is no clinical tool to predict incident PAD in SA patients. The CHADS2 score has been found useful in predicting PAD risk. This study was designed to investigate the association between these diseases and the usefulness of CHADS2 and CHA2DS2ASc scores in predicting subsequent PAD in SA patients. From a population-based database of one-million representative subjects, adult patients with SA diagnosis were enrolled as the suspected SA group, and those having SA diagnosis after polysomnography were further extracted as the probable SA group. Twenty sex- and age-matched control subjects were randomly selected for each SA patients. The occurrence of PAD after SA was taken as the primary endpoint. Totally, 10,702 and 4242 patients were enrolled in the suspected and probable SA groups, respectively. The cumulative incidence of PAD was similar between SA patients and the corresponding control groups. Multivariable Cox regression analyses showed that SA was not an independent risk factor for subsequent PAD. Sensitivity analyses using propensity score-matched cohorts showed consistent results. Furthermore, in stratifying the SA patients by CHADS2, CHA2DS2ASc, or a newly-proposed ABCD (composed of Age, high Blood pressure, Cerebral vascular disease, and Diabetes mellitus) score, patients with higher scores predicted higher risks of subsequent PAD, while the ABCD score appeared to be the most robust. Aggressive risk modification is suggested to reduce the subsequent PAD risk in SA patients with a higher CHADS2, CHA2DS2ASc, or ABCD score.