Periodontal tissue engineering based on cell replacement therapies is a promising field for improved regeneration of tooth supporting structures lost as a result of destructive periodontal diseases. Human embryonic stem cells (hESCs) could become adequate cell source for tissue engineering because of their unlimited proliferative potential and ability to differentiate to all somatic cell types. The aim of this study was to analyze the differentiation capacity of hESCs toward periodontal compartment cells and their relationship with tooth root surfaces in vitro. Periodontal ligament fibroblastic cell (PDLF) cultures were established and characterized; hESCs (HUES-9 line) were expanded in undifferentiated state and characterized for pluripotency morphologically and immunohistochemically. Extracted tooth root slices (RS) of 300 mm thickness, prepared with both periodontal and endodontic instrumentation, were used. Three different experimental groups were established: (i) undifferentiated hESC colonies cultured on and around the RS; (ii) undifferentiated hESC colonies cultured on and around RS with PDLF coculture, and (iii) undifferentiated hESC colonies cultured on and around RS with PDLF coculture in osteoinductive medium for 3 weeks. The fibrogenic and osteogenic marker expression was assessed with immunohistochemistry; histological staining and scanning electron microscopy were utilized to determine the relationship between differentiating hESCs and mineralized tooth root structures. Results demonstrate that hESC differentiation is influenced by tooth structures, PDLFs, and osteogenic medium, resulting with increased propensity toward mesenchymal lineage commitment, and formation of soft-hard tissue relationship in close contact areas. The proposed experimental system may facilitate further understanding in development of periodontal structures and contribute to realization of hESCs as a cell source in periodontal tissue engineering applications.