Equine cord blood-derived mesenchymal stem cells (eCB-MSC) were cultured within coralline hydroxyapatite scaffolds in order to evaluate their suitability in bone tissue engineering applications. The MIT cell proliferation assay showed that undifferentiated eCB-MSCs have the capacity to undergo cell proliferation within three-dimensional (3D) constructs when cultured in expansion medium. DAPI nuclear fluorescence staining and scanning electron microscopy visualized the distribution and attachment of these cells to the scaffold microstructure. Osteogenic potential was evaluated by the detection of osteogenic markers such as RunX2, osteopontin, osteonectin, and increased levels of alkaline phosphatase activity in scaffolds cultured in medium containing known osteogenic differentiation factors. Bone matrix mineralization was identified by increased osteocalcin protein production in the culture medium containing induced scaffolds. These results demonstrate that eCB-MSC-seeded scaffolds may be potentially used as a future treatment for selected bone-gap defects that occur in race, pleasure, and working horses.