Background This study compared the pulmonary embolism (PE) risks between Asian dialysis patients and a comparison cohort without clinical kidney disease. Methods From the National Health Insurance claims data of Taiwan, we identified 106 231 newly diagnosed end-stage renal disease patients undergoing dialysis in 1998-2010 and randomly selected 106 231 comparison subjects, frequency matched by age, sex and the index year. We further selected 7430 peritoneal dialysis (PD) patients and 7340 propensity score-matched hemodialysis (HD) patients. Incidence rates and hazard ratios (HRs) of PE and odds ratio (OR) of subsequent 30-day deaths from PE were evaluated among study cohorts by the end of 2011. Results The overall incident PE was nearly 3-fold greater in dialysis patients than in the comparison cohort (0.92 versus 0.33 per 1000 person-years), with an adjusted HR of 2.02 [95% confidence interval (CI) = 1.63-2.50]. The PE incidence was greater in the propensity score-matched HD patients, than in PD patients with an adjusted HR of 2.30 (95% CI = 1.23-4.29). There was a greater PE risk for central venous catheter users than non-users among HD patients (1.83 versus 0.75 per 1000 person-years). The 30-day mortality from PE was higher in dialysis patients than in the comparison cohort (16.5 versus 9.77%) with an adjusted OR of 2.56 (95% CI = 1.32-4.95). Conclusions Dialysis patients are at a nearly 2-fold increased hazard of developing PE and are at greater risk of fatality from PE compared with those without clinical kidney disease. This study also shows a higher PE risk in HD patients than in PD patients.