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Abstract Background Our aim was to construct a diagnostic model for ruling out chronic thromboembolic pulmonary hypertension (CTEPH) in symptomatic patients after acute pulmonary embolism (PE) that is based on simple, non-invasive tests. Methods Plasma levels of various CTEPH associated biomarkers and conventional ECG criteria for right ventricular pressure overload were assessed in 82 consecutive patients with confirmed CTEPH and 160 consecutive patients with a history of PE who were suspected to have CTEPH, but in whom this disease was ruled out. Results ECG criteria of right ventricular hypertrophy were detected more frequently in patients with CTEPH (77%) than in the patients without CTEPH (11%, Odds ratio 26, 95% confidence interval [CI] 13–53). Also, clotting factor FVIII activity and the levels of N-terminal-pro-brain-type natriuretic peptide (NT-pro-BNP), Growth Differentiation Factor-15, C-reactive protein and urate, but not D-dimer level, were higher in patients with CTEPH. A diagnostic model including ECG criteria and NT-pro-BNP levels had a sensitivity of 94% (95% CI 86-98%) and a specificity of 65% (95% CI 56-72%). The area under the receiver-operator-characteristic curve was 0.80 (95% CI 0.74-0.85) for the diagnosis of CTEPH. Even with high disease prevalences of up to 10%, the negative predictive value of this model proved to be very high (99%, 95% CI 97-100%). Conclusions Ruling out CTEPH in patients after acute PE seems to be safe without additional diagnostic testing in absence of ECG criteria indicative of right ventricular hypertrophy and a normal NT-pro-BNP level.