Extracting and concentrating mitochondrial protein complexes from gel strips after blue native PAGE (BN-PAGE) can be daunting tasks using the traditional methods, such as electroelution, passive diffusion and centrifugal concentration. We present a simplified gel electrophoresis method to concentrate mitochondrial protein complexes with excellent recovery rate. Mitochondrial complex I present in a long gel strip from BN-PAGE can be easily concentrated into a 0.8 cm gel strip when a second BN-PAGE is performed with a Y-shaped gel and the addition of 0.01% n-dodecyl beta-D-maltoside and 0.001% SDS in the cathode buffer. Once completed, the concentrated protein complex in the gel strip is ready for SDS-PAGE or proteomic studies.