The factors that contribute to pulmonary embolism (PE), a potentially fatal complication of deep vein thrombosis (DVT), remain poorly understood. Whereas fibrin clot structure and functional properties have been implicated in the pathology of venous thromboembolism and the risk for cardiovascular complications, their significance in PE remain incomplete. Therefore we systematically compared and quantified clot formation and lysis time, plasminogen levels, viscoelastic properties, activated factor XIII crosslinking and fibrin clot structure in isolated DVT and PE subjects. Clots made from plasma of PE subjects showed faster clot lysis times with no differences in lag time, rate of clot formation or maximum absorbance of turbidity as compared to DVT. Differences in lysis times were not due to alterations in plasminogen levels. Compared with DVT, clots derived from PE subjects showed accelerated establishment of viscoelastic properties, documented by a decrease in lag time and an increase in the rate of viscoelastic property formation. The rate and extent of fibrin crosslinking by activated factor XIII were similar between clots from DVT and PE subjects. Evaluation by electron microscopy revealed that plasma fibrin clots from PE subjects exhibited lower fiber density compared to those from DVT subjects. These data suggest that clot structure and functional properties differ between DVT and PE subjects and provide insights into mechanisms that may regulate embolization.