The mammalian SWI/SNF chromatin-remodeling complex, also called BAF (Brg1/Brm associated factor) complex, is known to be involved in a variety of cellular processes, including differentiation, proliferation as well as oncogenesis. Embryonic stem (ES) cell-specific BAF (esBAF) complex is known to regulate two major characteristics of ES cells, pluripotency and self-renewal capacity. Baf53a is one of the important components of esBAF complex, and here we investigated chromatin remodeling factor Baf53a functions in mouse ES cells. In our study, we established tetracycline-inducible Baf53a conditional knockout (KO) ES cells. Western bolt analysis showed that self-renewal marker genes, including Nanog, Oct3/4, Dax1, and Esrrb, were expressed in Baf53a KO ES cells. Proliferation assays (direct cell counts and WST-1 assay) revealed that cell growth of Baf53a KO ES cells was completely repressed ; and p53, p21 and cleaved caspase 3 were induced in Baf53a deficient ES cells. Colony formation assay revealed that Baf53a depletion resulted in ES cell colonies disappeared; however, colony formations were rescued by an artificial expression of Baf53a, but not Baf53a M3 mutant (E388A/R389A/R390A, a dominant lethal mutant form in yeast) in Baf53a KO ES cells. Interestingly, colony formation of Baf53a KO ES cells was recovered by forced expression of Baf53b, a homologue of Baf53a. Furthermore, Baf53a- or Baf53b-expressing Baf53a KO ES cells exhibited normal proliferation with repression of p21 expression. In addition, these cells expressed self-renewal marker genes (Nanog, Oct3/4, Esrrb, Klf4 and Rex1) and exhibited alkaline phosphatase activity, which is the marker for undifferentiated state of ES cells. Taken together, our findings suggest that Baf53a, one component of esBAF complex, regulates cell growth process by regulating p53-p21 pathway and Caspase3 activity; and Baf53b exhibited the redundant function of Baf53a in mouse ES cells.