Abstract Background Troponin I (cTnI), myoglobin, heart-type fatty acid binding protein (H-FABP), and natriuretic peptides (BNP, NTproBNP) were all reported to be elevated in patients with pulmonary embolism (PE). Methods To assess the correlation between the aforementioned markers and helical computed tomography (hCT) right ventricular dysfunction (RVD) in non massive PE, we performed this prospective pilot study on 50 patients. Results Patients with RVD had significant higher natriuretic peptides prevalence than cardiomyocytes damage-related markers (48% vs 20%, P = 0.006). Significant prevalence differences were observed only for natriuretic peptides when patients with RVD and those without were compared (74% vs 33% for NT-pro BNP, P = 0.005 and 65% vs 22% for BNP, P = 0.003). Patients with RVD had significant higher biomarkers median plasmatic values than those without (BNP: 170 vs 36 pg/ml, P = 0.0027; NT-proBNP: 1369 vs 170.7 pg/ml, P = 0.0024; cTnI: 0.032 vs 0 ng/ml, P = 0.0034; H-FABP: 4.32 vs 2.23 ng/ml, P = 0.0032; myoglobin: 36.7 vs 28.2 ng/ml, P = 0.03). Significant correlations were only obtained between RV/LV index and plasmatic natriuretic peptides (NT-proBNP: r = 0.36, P = 0.009; BNP r = 0.28; P = 0.047). Conclusions Natriuretic peptides prevalence elevation and median values are significantly higher when RVD is present and significantly correlate with hCT RVD.