The commonly practiced removal of granulation tissue during periodontal surgery, aiming to eliminate infection and optimize healing conditions, may also remove progenitor stem cells that could otherwise support periodontal regeneration. The present study aimed to investigate if cells with embryonic stem cell properties are present in periodontal granulation tissue. During the course of flap surgery inflammatory granulation tissue was obtained from four patients and five periodontal defects. Tissues were processed in a collagenase/dispase solution to release the cells. Part of the resulting suspension was processed for bacteriological analysis (IAI PadoTest 4.5), whereas the remaining cell suspension was cultured and passaged once. Upon reaching confluence, total RNA was extracted, followed by cDNA synthesis. PCR was then performed (SYBR Green-based protocols) to measure gene expression levels of Collagen type I, and embryonic stem cell markers Nanog, Oct4, Rex-1 and Sox2. Results are expressed as 2⁻Δ(Ct) values of the target gene, calibrated against a house-keeping gene (GAPDH). A high total bacterial load up to 20.6 ± 11.0×10(6) counts/mg of tissue was found. Collagen type I was strongly expressed, confirming the predominance of mesenchymal/fibroblastic cells. Among the studied embryonic stem cells markers, Nanog was most highly expressed (2.3 ± 1.2), followed by Oct4 (1.1 ± 0.5), Rex-1 (0.6 ± 0.2) and Sox2 (0.3 ± 0.2). This is the first study that demonstrates the presence of cells expressing embryonic stem cell markers among infected granulation tissue. This knowledge needs to be considered when devising future strategies to improve periodontal wound healing and regeneration.