It remains unclear how superantigen induces unresponsiveness in stimulated T cells. We analyzed the chromatin status of the interleukin-2 (IL-2) promoter region in T cells stimulated with toxic shock syndrome toxin-1 (TSST-1) superantigen using T cell receptor-transgenic T cells responding to ovalbumin (OVA) and TSST-1. Compared to OVA stimulation, naïve T cells cultured with TSST-1 showed lower IL-2 expression after transient enhancement. Coincidentally, the acetylated histone H3 (AcH3) level at the IL-2 promoter region was first enhanced, and then decreased, in TSST-1-stimulated T cells. At the reduction stage of AcH3, histone deacetylase-1 (HDAC1) was markedly associated with the IL-2 promoter region in a TSST-1-specific manner without HDAC1 over-expression. The enhancement of HDAC1 association and IL-2 suppression was prevented by pre-treatment with HDAC inhibitor, but not once the anergy status was established. These results suggest that recruitment of HDAC1 in the IL-2 promoter region at the early stimulation stage with TSST-1 plays a pivotal role in sAg-induced anergy.