Our study aimed to determine the incidence and severity of obstructive sleep apnea (OSA) in patients with end-stage renal disease (ESRD) and also whether different dialysis modalities confer different risk and treatment response for OSA. We used Taiwan’s National Health Insurance Research Database for analysis and identified 29,561 incident dialysis patients as the study cohort between 2000 and 2011. Each dialysis patient was matched with four non-dialysis control cases by age, sex, and index date. Cox regression hazard models were used to identify the risk of OSA. The incidence rate of OSA was higher in the peritoneal dialysis (PD) cohort than the hemodialysis (HD) and control cohort (18.9, 7.03 vs. 5.5 per 10,000 person-years, respectively). The risk of OSA was significantly higher in the PD (crude subhazard ratio (cSHR) 3.50 [95% CI 2.71–4.50], p < 0.001) and HD cohort (cSHR 1.31 [95% CI 1.00–1.72], p < 0.05) compared with the control cohort. Independent risk factors for OSA in this population were age, sex, having coronary artery disease (CAD), hyperlipidemia, chronic obstructive pulmonary disease (COPD), and hypertension. Major OSA (MOSA) occurred in 68.6% in PD and 50.0% in HD patients with OSA. In the PD subgroup, the incidence of mortality was significantly higher in OSA patients without continuous positive airway pressure (CPAP) treatment compared with OSA patients undergoing CPAP treatment. The results of this study indicate that ESRD patients were at higher risk for OSA, especially PD patients, compared with control. The severity of OSA was higher in PD patients than HD patients. Treatment of MOSA with CPAP was associated with reduced mortality in PD patients.