Deep vein thrombosis (DVT) is a common disorder that is associated with high morbidity and mortality. Genetic factors have been suggested to influence the predisposition towards thrombosis and the incidence of DVT. Platelet endothelial cell adhesion molecule-1 (PECAM-1) is a key adhesion molecule that is involved in platelet function and maintenance of endothelial cell junctions. To date, no studies have examined the association between polymorphisms in PECAM-1 and DVT. The present study analyzed the single nucleotide polymorphisms (SNPs) of PECAM-1, namely Leu125Val (C373G), Asn563Ser (T1688C) and Gly670Arg (C2008T), in Chinese patients with DVT and age-and gender-matched controls, using polymerase chain reaction-restriction fragment length polymorphism analysis. Furthermore, plasma soluble PECAM-1 (sPECAM-1) levels were quantified by ELISA. The results of the present study demonstrated significantly higher genotype and allele frequencies of the Leu125Val polymorphism in PECAM-1 in the DVT group as compared with those in the control group (P<0.05). The plasma levels of sPECAM-1 in the DVT group (83.4 ± 23.5 ng/ml) were also significantly higher as compared with those in the control group (60.4 ± 19.4 ng/ml, P<0.01). In the patients with DVT, plasma levels of sPECAM-1 were significantly higher in those with the Leu/Val and Val/Val genotypes as compared with those possessing the Leu/Leu genotype (P<0.05). The PECAM-1 Leu125Val polymorphism was shown to be associated with an increased risk of DVT and PECAM-1 protein expression levels in venous vessels. In patients with DVT, the PECAM-1 Leu/Val and Val/Val genotypes were associated with delayed thrombus resolution, as determined by thrombus scoring, as compared with that in patients possessing the Leu/Val genotype. In conclusion, the present study indicated that PECAM-1 Leu125Val polymorphism and sPECAM-1 levels may be associated with DVT.