Increasing availability of micro-computed tomography (μCT) as a structural imaging gold-standard is bringing unprecedented geometric detail to soft tissue modeling. However, the utility of these advances is severely hindered without analogous enhancement to the associated kinematic detail. To this end, labeling and following discrete points on a tissue across various deformation states is a well-established approach. Still, existing techniques suffer limitations when applied to complex geometries and large deformations and strains. Therefore, we herein developed a non-destructive system for applying fiducial markers (minimum diameter: 500μm) to soft tissue and tracking them through multiple loading conditions by μCT. Using a novel applicator to minimize adhesive usage, four distinct marker materials were resolvable from both tissue and one another, without image artifacts. No impact on tissue stiffness was observed. μCT addressed accuracy limitations of stereophotogrammetry (inter-method positional error 1.2±0.3mm, given marker diameter 1.9±0.1mm). Marker application to ovine mitral valves revealed leaflet Almansi areal strains (45±4%) closely matching literature values, and provided radiographic access to previously inaccessible regions, such as the leaflet coaptation zone. This system may meaningfully support mechanical characterization of numerous tissues or biomaterials, as well as tissue-device interaction studies for regulatory standards purposes.