Abstract. The mouse ischemic hindlimb model is used widely for studying collateral artery growth (i.e., arteriogenesis) in response to increased shear stress. Nonetheless, precise measurements of regional shear stress changes along individual collateral arteries are lacking. Our goal is to develop and verify trans-illumination laser speckle flowmetry (LSF) for this purpose. Studies of defibrinated bovine blood flow through tubes embedded in tissue-mimicking phantoms indicate that trans-illumination LSF better maintains sensitivity with an increasing tissue depth when compared to epi-illumination, with an ∼50% reduction in the exponential decay of the speckle velocity signal. Applying trans-illuminated LSF to the gracilis muscle collateral artery network in vivo yields both improved sensitivity and reduced noise when compared to epi-illumination. Trans-illuminated LSF images reveal regional differences in collateral artery blood velocity after femoral artery ligation and are used to measure an ∼2-fold increase in the shear stress at the entrance regions to the muscle. We believe these represent the first direct measurements of regional shear stress changes in individual mouse collateral arteries. The ability to capture deeper vascular signals using a trans-illumination configuration for LSF may expand the current applications for LSF, which could have bearing on determining how shear stress magnitude and direction regulate arteriogenesis. © The Authors.Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.