The use of allogeneic stem cells strongly extends the range of stem cell applications in dentistry; however, immunological rejection remains a major concern. There is little information about the immunological features of dental-related stem cells in the literature. Therefore, we investigated the immunological characteristics of stem cells from the root apical papilla (SCAP) of swine in vitro by measuring T cell immunomodulation and apoptosis. We found that SCAP expressed a low level of swine leukocyte antigen (SLA) class I molecules and were negative for SLA class II DR molecules. Moreover, SCAP could inhibit autologous T cell proliferation stimulated by phytohemagglutinin (PHA) and a one-way mixed lymphocyte reaction in a dose-dependent manner. In addition, SCAP could suppress proliferation of allogeneic T cells in a dose-dependent manner, with or without mitomycin C pretreatment. Moreover, soluble factor(s) may be involved in the SCAP-mediated immune suppression. After a 5-day coculture of SCAP, allogeneic T cells, and PHA, only 1.22% of T cells were apoptotic. These data indicated that SCAP were weakly immunogenic and suppressed T cell proliferation in vitro through an apoptosis-independent mechanism.