Using the program Protein Blast, we analyzed nuclear proteins of seven species, from yeast to human, the proteins of synaptonemal and cohesin complexes, histones, meiotic enzymes, tubulins, and membrane proteins. The amino acid sequences were compared with the sequences of the proteins from archaeal and bacterial proteomes; random sequences were used as a control. It was found that nuclear proteins of eukaryotes show similarity with archaeal proteins, as well as somewhat lower similarity with bacterial proteins; this favors the hypothesis about the mixed origin of the eukaryotic nucleus. It should be noted, however, that similarity of the studied eukaryotic proteins with prokaryotic ones is rather low. Many eukaryotic proteins have no related proteins in prokaryotic proteomes; this suggests de novo origin of many proteins in the course of evolution of the ancient eukaryotes.