Manganese (Mn) is accumulated in the nuclear and mitochondrial fractions when excess Mn is administered. However, little is known with respect to the behaviors of Mn in nuclei. In the present study, rats were given excess Mn and the nuclei were purified from liver cells by differential and sucrose gradient centrifugations. Being subjected to equilibrium dialysis with a radioactive 54Mn, the binding capacity of Mn in nuclei from the control rat was five-fold higher than BSA, which was used as a reference protein; and the capacity of 54Mn-binding rose in the nuclei from the Mn-treated animals in comparison with those from the control. On the analyses of nuclear materials with partial solubilization, sepharose column chromatography and HPLC, there were two major fractions which associated with a lot of Mn; one fraction was of large molecules of DNA, and the other fraction seemed to be peptides with small molecular weights. Therefore, Mn may open up a superhelical structure of DNA to provide more negatively charged phosphate moiety as a binding-site for a positively charged Mn. The results also disclosed a possible aberration in biological functions due to excess Mn in nuclei; the apparent association constant of triiodothyronine, a physiologically active thyroid hormone, to the nucleus was reduced by 75% and the uptake of 14C-labelled orotic acid to a newly synthesized RNA in the liver was severely inhibited.