Fractionation and extraction of nuclear proteins are techniques intended to facilitate dedicated plant proteomic studies. These techniques rely on subcellular fractionation, which makes it possible to define and characterize the proteome of a subcellular organelle, in this case the cell nucleus. Nuclear protein fractionation is proposed as a method to be carried out according to the solubility of proteins in buffers of increasing ionic strength. This physical criterion, accompanied in some steps by the use of additional reagents, such as detergents or enzymes, produces fractions that have been demonstrated to have functional significance. The proposed procedure yields five fractions, the first of them containing proteins associated with the nuclear envelope and remnants of the cytoskeleton. The second fraction, which is soluble at low ionic strength, contains ribonucleoproteins active in nuclear RNA metabolism. After increasing ionic strength and digesting with DNase, the result is the chromatin fraction. Finally, the fourth and fifth fractions correspond to the nuclear matrix and are obtained, respectively, by solubilization in high salt concentration and in the form of the residual pellet, which is only soluble in 7 M urea under sonication. This procedure offers a wide range of applicability, even in the cases in which the genome of the particular species investigated is not sequenced. In general, the functional criteria driving the extraction method described here will make this method capable of generating valuable and useful information.