The subjects of the study were 94 patients with pulmonary arterial thromboembolism (PATE). The prevalence of thrombophilic conditions (TC) among these patients was studied, and their role in the development of an unfavorable clinical course of PATE was evaluated. A three-year prospective study revealed that pre-thrombotic conditions had been diagnosed in 90% of PATE patients. There is a strong correlation between an unfavorable course of PATE and the presence of isolated or combined genetic mutations, or a combination of those with an increase of factor VIII level, and a high titer of cardiolipin antibodies with a mutation in factor V gene. Occurrence of PATE in patients less than 40 years of age who suffer from an idiopathic type of venous thrombosis and have a family background of thrombophilic conditions, which requires a detailed hematological examination, is a predictor of unfavorable course of PATE in the post-hospital period. Purposeful pharmaceutical correction of thrombophilic conditions lowers the frequency of venous thrombosis recurrence from 39% to 17%, the frequency of cava-filter thrombosis recurrence from 24% to 3.7%, and the frequency of PATE recurrence from 15% to 5.6%.