DNA-dependent RNA polymerase II has been purified to high specific activity and apparent homogeneity from both calf thymus and rat liver. Two form II enzymes are present in rat-liver preparations, one with the molecular structure 1(190,000)i(150,000),(35,000)1(25,000)dl, the other with a molecular structureof [(170,000),(150,000) -(35,000),(25,000),] (molecular weights are within ±5% but the absolute values are approximate). Inclusion of a proteolytic inhibitor during the isolation procedure decreases the proportion of the molecule containing the 170,000 subunit. Calf-thymus RNA polymerase preparations typically exhibit four components on polyacrylamide gels that contain sodium dodecyl sulfate, with an apparent molecular structure of [(190,000)1(150,000),(35,000)1-(25,000)i]. In addition, some calf-thymus polymerase II preparations contain small quantities of the [(170,OO)1-(150,000)i(35,000)1(25,000)iJ species; the quantity of this species may also be increased from less than 5% in the normal preparation to at least 40% in an "aged" preparation. Thus, the 170,000 subunit may be derived from the 190,000 subunit in both tissues. Until unequivocal evidence is obtained on this point, however, the possibility that the large subunits are unique species should not be eliminated. The general structural similarity of the eukaryotic RNA polymerase II with that of the prokaryotic polymerase suggests that the modes of action and regulation may be analogous.Multiple forms of DNA-dependent RNA polymerases have been shown to exist in eukaryotic cells (1, 2). Polymerase I is localized in the nucleolus (2); its RNA product has the base composition and hybridization behavior expected of ribosomal RNA (3). These data indicate that the major role of this enzyme is to synthesize ribosomal RNA, although it may transcribe a limited number of other RNA species. Polymerase II, on the other hand, is found in the nucleoplasm (2). Its product has a more DNA-like base composition and is competed well in hybridization-competition experiments by whole nuclear RNA (3), suggesting that this polymerase synthesizes the bulk of the nucleoplasmic RNA species. A role for polymerase III, believed to be present in the nucleoplasm, has yet to be elucidated. The mushroom toxin, aamanitin, selectively inhibits polymerase II, while forms I and III are not affected (4,5