Metastasis most commonly occurs in the liver, lung, bone, and brain, implying its preference for specific organs. We hypothesized that organ microcirculation coagulation environment predisposes to tumor cell retention. Coagulation factors were analyzed using immunostaining, enzyme-linked immunosorbent assay, and heparanase procoagulant activity assay. In normal mice, expression levels of heparanase, tissue factor (TF), TF pathway inhibitor (TFPI), and TFPI-2 were low in the microcirculation of the liver, lung, brain cortex, and bone, and high in the microcirculation of the subcutis, skeletal muscle, brain subcortex, and bone marrow. C57BL/6 mice injected s.c. with B16 (F10) melanoma cells demonstrated lower levels of heparanase, TF, TFPI, and TFPI-2 in metastasis blood vessels compared to those in the primary tumor. In these mice with metastasis, liver and lung microcirculation turned to express high levels of coagulation proteins. Additionally, although mice with heparanase overexpression developed a larger primary tumor, they did not demonstrate a tendency for metastasis, as opposed to controls (P < 0.0001). Human umbilical vein endothelial cells, incubated with the B16 melanoma cell medium for 2 hours, expressed decreased levels of heparanase, TF, TFPI, and TFPI-2, and the effect was reversed by a peptide-inhibiting heparanase/TF complex interaction (P < 0.001). In summary, metastasis has a predilection to organs with low levels of heparanase, TF, TFPI, and TFPI-2 in the microcirculation, which enables tumor cell retention. Heparanase has a role in regulating the microcirculation milieu.