In order to separate all protein components of muscle nuclei, three types of two-dimensional gel electrophoresis were tried to find out advantages and disadvantages in them. Non-equilibrium pH gradient electrophoresis gave a reasonably good pattern, but a large amount of proteins left unanalyzed on the acidic top of the gel. Isoelectric focusing of nuclear proteins extracted with SDS gave a pattern lacking proteins in acidic area, although histones were well separated. Isoelectric focusing with agarose gels in the first dimension separated almost all protein components of muscle nuclei in wide ranges of molecular size (10-400kD) and pI (3.7-9.5), leaving histones in the area of pH over 9.5.