BEX2 (Brain expressed X-linked protein 2), a 13 kDa protein, is highly expressed in brain and testis. It is reported that the protein expression of BEX2 dramatically alters during the embryo development, but little is known about its function. By means of yeast two-hybrid screening, we isolated that INI1/hSNF5 was a binding partner for BEX2, a key component of SWI/SNF chromosome remolding complex. GST Pull-down experiment interaction is physical and specific. Further analysis using truncated mutations demonstrated that the two partner for BEX2, a key component of SWI/SNF chromosome remolding complex. GST Pull-down experiment confirmed that BEX2 can interact with INI1/hSNF5 directly and specifically. Truncated mutations analysis further demonstrated that the two conserved reverse repeats sequences within INI1/hSNF5 were necessary for the interaction. Sub-cellular localization showed that both BEX2 and INI1/hSNF5 mainly localized in cell nucleus, which indicated that the interaction may be involved in the regulation of gene expression. Our experiments also showed that co-overexpressing of the two proteins affected cell cycle by increasing the cells in S phase, indicating that BEX2 could regulate cell cycle by interacting with INI1/hSNF5.