Cleaved fragments of the extracellular matrix protein perlecan have been shown to promote neuroprotection and repair after ischemic stroke. The cysteine proteases cathepsin B and L as well as the metalloprotease bone morphogenic protein 1 (BMP-1) are capable of releasing the biologically active C-terminal laminin-like globular domain (LG3) of perlecan. Exercise, a known method of reducing stroke risk and severity, has been shown to increase the expression of some proteases associated with perlecan processing. Using a transient distal middle cerebral artery occlusion (MCAo) model for focal ischemic stroke we show that while 7 days of running only slightly decreased infarct volume, BMP1 and perlecan (HSPG2) RNA expression in skeletal muscle was significantly increased in 3-month-old male wild type C57/BL6 mice. Moreover, elevated levels of BMP1 RNA were still detectable after 3 days of detraining, suggesting a prolonged effect of exercise on BMP1 expression. Levels of LG3 in the blood were below the limit of detection in the current study, however it is likely that a more sensitive method would enable analysis of serum. These preliminary findings suggest that LG3 could be a molecular mediator of neuroprotection afforded by exercise though further studies are required.