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Objective To explore whether there are stem cells in the endosalpinx, and to compare the biological properties between the mucosal stem cells (MuSCs) and mesenchymal stem cells (MeSCs) obtained from the fallopian tube for the purpose of providing experimental basis for clinical application. Methods In this study, we isolated, cultured and amplified human MuSCs and MeSCs in vitro, and compared the cell morphology, cell phenotype, colony forming efficiency, proliferation and differentiation capacities of MuSCs and MeSCs. Results Both MeSCs and MuSCs showed a similar elongated morphology, but the arrangement of MuSCs were more uniform than that of MeSCs. MuSCs showed a significantly higher proliferation capacity compared with MeSCs. Colony forming unit-fibroblast analysis further showed that more colonies formed with MuSCs than that of MeSCs, with a significant statistical difference. However, FTMSC and FMSC showed similar immunophenotypes. In vitro assays revealed that both types of cells showed the potential of adipogenic, osteogenic, and chondrogenic differentiation. Conclusions Stem cells were found in the fallopian tube mucosa, and MuSCs have stronger proliferation capacity than MeSCs, thus they possess a higher value for clinical application. DOI: 10.11855/j.issn.0577-7402.2015.04.08