The use of stem cells from the apical papilla (SCAPs) has been proposed for promoting root maturation in permanent immature teeth and has a significant role in regenerative dental procedures. However, SCAP’s role may be compromised by microenvironmental factors such as hypoxic conditions and the presence of bacteria from infected dental root canals. We aim to investigate the transcriptome profile of SCAPs from 3 donors with or without oral bacteria stimulation.