In the present study, we compared groups of patients with and without thrombophilia, who underwent pulmonary endarterectomy (PEA), definitive treatment for chronic pulmonary hypertension resulting from thromboembolic disease.Between September 2004 and June 2007, we operated 54 patients with CTEPH. We divided our patients into three groups. Group I patients, had one or more signs of serious thrombophilia (15 patients), Group II patients, had no signs of thrombophilia (23 patients without thrombophilia and without Methylenetetrahydrofolate Reductase (MTHFR)), and Group III patients with MTHFR (16 patients with MTHFR only, without any serious thrombophilia).After the surgery, there was a statistically considerable improvement of hemodynamic parameters (mPA, CI, PVR) in all groups, without a statistical difference between the groups. Comparison of all these groups showed more complications in-group I (thrombophilia), in particular reperfusion oedema, pericardial effusion, and renal insufficiency. Within one month, there was a considerable improvement or normalisation of haemodynamic parameters, an increase in walking distance at the six-minute walking test, and NYHA classification with no significant difference between the three groups.Early hemodynamic results of patients with thrombophilia after PEA, were comparable to the results of patients without thrombophilia, when we looked at both clinical and hemodynamic improvements. We did not find any differences when we looked at the results between Group II and Group III (MTHF), when we considered the number and type of complications. Patients with thrombophilia in Group I had statistically higher morbidity, especially when it came to a higher number of reperfusion oedema, pericardial effusion, and renal insufficiency.