The aim of this study was to compare whole-genome gene expressions of periodontal ligament (PDL) and pulp (P) mesenchymal stem cells (MSCs) isolated from third molar (m), premolar (p), and deciduous (dec) teeth. Total RNAs were isolated and used for cRNA synthesis. Human Expression Hybridization Assay was used for 47,000 probes. Data were subjected to quantile normalization before analysis. Based on the differentially expressed genes, immunomodulation properties of m/p/dec-MSCs were evaluated. Lymphocytes cocultured P/pdl-MSCs were investigated for apoptosis and cell survival of phytohemagglutinin-stimulated T cells. T cells and medium supernatants were collected on Days 1 and 4 of the experiments to evaluate T-cell proliferation by WST-1 and apoptotic markers by flow cytometry. Statistical analysis demonstrated that 291 genes were differentially expressed ≥2 fold in the cells isolated from p/m/dec, and pdl/P MSCs. The most significant difference was recognized in the proenkephalin (PENK) gene (24-fold) in pPDLMSCs, epidermal growth factor-like protein 6 (EGFL6), and complement factor D (CFD) genes were differentially expressed in decPMSCs 16.9-fold and 11-fold, respectively, when compared to other MSCs. A difference in PENK mRNA expression was also confirmed by RT-PCR. Findings of the study revealed that all dental MSCs cocultured with T cells suppressed the proliferation of T cells on Day 1 when compared to T cells alone (p = 0.001). The suppression of T lymphocytes proliferation, PENK, and IL-10 mRNA expressions was higher in pPDLMSCs. Highest PENK and IL10 mRNA expressions and T-cell regulation in PDLMSCs suggested that PDLMSCs might be a promising candidate for immune regulation.