To compare characterization of microRNAs (miRNAs) expression profiles of induced pluripotent stem cells (iPSCs) reprogrammed from human dental pulp stem cells (DPSCs) and stem cells from apical papilla (SCAP) and screen-specific microRNA.Human DPSCs and SCAP were reprogrammed into iPSCs using a Sendai virus vector. Total RNA of human DPSCs-iPSCs and SCAP-iPSCs were extracted. miRNAs were labeled and hybridized. Slides were scanned, and images were imported into GenePix Pro 6.0 for grid alignment and data extraction. Significant differentially expressed miRNAs between the two groups were identified using fold change and P-value and were analyzed.Both human DPSCs and SCAP were successfully reprogrammed into iPSCs. Among miRNA genes analyzed by miRNA microarray, 68 were differentially expressed by more than 10-fold in DPSCs-iPSCs; 37 of these genes were up-regulated, and 31 were down-regulated. In SCAP-iPSCs, 107 genes were differentially expressed by more than 10-fold; 68 were up-regulated, and 39 were down-regulated. In both cells, only miR-302e was up-regulated, whereas 9 miRNAs were down-regulated: miR-29b-3p, miR-181b-5p, miR-4328, miR-22-5p, miR-145-5p, miR-4324, let-7b-5p, miR-181a-5p, and miR-27b-3p.Multiple miRNAs participated in reprogramming of human DPSCs and SCAP into iPSCs. Most miRNAs are related to cell cycle, transforming growth factor-β signaling pathways and epithelial-mesenchymal transition.