Collagen is believed to be one of the principal load bearing components of skin. This implies that deformation of collagen microfibrils play an important role in determining the extent of skin deformation under applied loads. We have developed a novel technique for generating internal strain maps of bundles of collagen microfibrils in the skin. The technique relies on digital image correlation (DIC) of second harmonic images of bundles of collagen fibrils obtained under different deformations. Applying the technique to mouse skin demonstrated a significant heterogeneity of deformation in the underlying collagen microfibrils. This technique can be used to evaluate the contribution of collagen to the biomechanical properties of skin in aging, disease, as well as in wound healing.