Thromboses of the cranial tibial vein (Horse 1) and brachial, median, and cranial circumflex humeral arteries (Horse 2) were identified as causes of unilateral lameness in two Thoroughbred racehorses. Nuclear scintigraphy was performed for suspicion of long bone stress fractures but instead allowed identification of unusual areas of increased radiopharmaceutical uptake within soft tissues of the affected limbs. Ultrasonography of these regions allowed identification of occlusive thrombi within a 25 cm length of the cranial tibial vein (Horse 1) and variable lengths of affected arteries in Horse 2. Horse 1 developed secondary infections and was euthanized. Staphylococcus aureus was isolated from all sites. The cause of thrombosis was not identified in Horse 2.