OBJECTIVE: In this paper we compared the two methods of cell sorting (magnetic cell sorting and flow cytometry sorting) for the isolation and function analysis of mouse CD4 CD25 regulatory T (Treg) cells, in order to inform further studies in Treg cell function. METHODS: We separately used magnetic cell sorting and flow cytometry sorting to identify CD4 CD25 Treg cells. After magnetic cell separation, we further used flow cytometry to analyze the purity of CD4 CD25 Treg cells, trypan blue staining to detect cell viability, and propidium iodide (PI) staining to assess the cell viability. We detected the immune inhibition of CD4 CD25 Treg cells in the in vitro proliferation experiments. RESULTS: The results showed that compared to flow cytometry sorting, magnetic cell sorting took more time and effort, but fewer live cells were obtained than with flow cytometry sorting. The CD4 CD25 Treg cells, however, obtained with both methods have similar immunosuppressive capacities. CONCLUSION: The result suggests that both methods can be used in isolating CD4 CD25 Treg cells, and one can select the best method according to specific needs and availability of the methodologies.