HDAC1, HDAC2 and RbAp46, RbAp48 are core subunits of several important functional molecular complexes, such as NuRD, Sin3. The four subunits interact with each other, forming a complex which has enzyme activity of deacetylation. However, little is known about the overall structure of this core complex and the influences of its structure to the chromatin deacetylation and remodeling activities. Here, we purified the HDAC1/2-RbAp46/48 core complex from the Sf9 cells infected with baculoviruses containing the genes of HDAC1, HDAC2, RbAp46, and RbAp48, and reconstructed the three dimensional architecture of the core complex using negative stain electron microscopic single particle analysis. It is found that the four subunits (HDAC1, HDAC2, RbAp46 RbAp48) can form a stable and uniform complex, but not all of the subunits exist in the form of a single copy or a proportion way in the the complex. It is shown that HDAC1/2-RbAp46/48 core complex presents an asymmetric saddle shape with a triangle shape back bulging. There is a groove, approximately 6 nm in width, in the middle of the wings of the saddle. We hypothesize that the groove is the binding site of the nucleosome, although further analysis is needed. The work reported here sheds a light on the overall structure of the HDAC1/2-RbAp46/48 complex and its interaction with nucleosome and chromatin, and the mechanism of deactylation enzyme activity of this core complex.