Conclusion The marked independent differences demonstrated in the B6 and A/J mice can be exploited to identify genetic determinants of thrombosis and haemostasis. Our results of the CSS screening suggest that novel or unknown genes can be used to identify the genes responsible for the traits related to arterial thrombosis, tail bleeding/rebleeding and vessel extracellular matrix. Identification of differences in the parent strains, such as those described in this study, and screening of the CSS is a first-step in the discovery of new genetic determinants of thrombotic risk.