Skeletal muscle comprises several fiber types classified based on their contractile and metabolic properties. Skeletal muscle fiber types are classified according to their myosin heavy chain isoforms (MyHC I, IIa, IIx, and IIb). We attained good separation of MyHC isoforms in a mini-gel system by modifying a previously developed electrophoresis protocol. Increased glycerol and decreased cross-linking agent concentrations improved the separation of MyHC isoforms. Sample preparation with dithiothreitol and protease inhibitors produced clear MyHC band boundaries. This protocol included silver staining, with a linear range. The protocol provided high resolution and a highly accurate assay of rodent MyHC isoforms.