Summary Background Pulmonary embolism (PE) is a potentially life-threatening condition that mainly affects the people of advanced age. While certain blood group phenotypes (non‑O blood group) are known risk factors for the development of venous thromboembolism (VTE), there is no research which investigated the association of blood group genotypes with severity of PE. The aim of this study was to investigate the frequency of ABO blood group genotypes among the population of patients with PE and to investigate the correlation of the pulmonary embolism severity index (PESI) score to specific ABO blood group genotypes. Material and methods In this cross-sectional study 74 patients with PE diagnosed using CT pulmonary angiography were included and 303 blood donors without VTE or congenital thrombophilia participated as a control group. After isolation of genomic DNA ABO blood group genotype was determined using the polymerase chain reaction sequence-specific amplification (PCR-SSP) method. Results We observed a significantly higher frequency of A1B and BB genotypes in patients with PE compared to healthy individuals (A1B 14.9% vs. 4.3%, P  < 0.001; BB 5.4% vs. 0.7%, P  = 0.004), while the O1O1 genotype was significantly less frequent in patients (24.3% vs. 37.3%, P  = 0.036). Analyzing the severity of the clinical presentation according to the PESI score, we did not find a correlation between the severity of the clinical presentation and a certain blood type genotype. Conclusion Patients with A1B and BB blood type genotype were at increased risk for developing pulmonary embolism, while patients with O1O1 genotype had a significantly lower risk of developing PE.