OBJECTIVES: To combine and supplement public national registries and patient level chart data in order to describe and compare demographics, treatment patterns and mortality in patients with chronic thromboembolic pulmonary hypertension (CTEPH), a rare disease. METHODS: Using the national Swedish prescription, inpatient and cause of death registries, CTEPH patients were identified via algorithms about drug prescriptions and diagnostic/procedural codes. A second cohort, identified from medical charts of diagnosed CTEPH patients treated in specialized treatment centers across five European countries was abstracted retrospectively. Descriptive statistics and potential areas of complementary information are described. RESULTS: Basic data on demographic and clinical characteristics, medication and selected health resource consumption data were found to have sufficient overlap to allow the comparison between cohorts.  From Swedish registries, 94 CTEPH patients were identified. In the medical charts, 116 patients were included. Mean age of 61.4±14.5 years in registry patients was 6.1 years younger than the chart cohort (67.5±12.3). Both cohorts were predominantly female (registry 52%, chart cohort 61%). Medications for pulmonary arterial hypertension were common in both datasets: endothelin receptor antagonists were 45% in registry versus 60% in chart, followed by phosphodiesterase-5 inhibitors (registry 36%, chart 32%), and prostacyclins were less common (5-6%).  Concomitant medications had similar patterns in both cohorts, as anticoagulants and diuretics were most frequently prescribed (registry 64%, 43%; chart 60%, 41%). Annualized mortality rate was slightly higher in the registry (9.9%) compared to the chart cohort (8.2%). Additional and complementary information was provided from chart abstraction, including: Frequency of outpatient visits, medical procedures/examinations and detailed clinical outcomes. CONCLUSIONS: Despite differences in data sources, these cohorts showed overall similarity in demographic characteristics, treatment patterns and clinical results. This approach supports the ability of supplementing nationally available register data with patient level data in order to broadly describe the burden of rare diseases like CTEPH.