Differential gel electrophoresis (DIGE) is based on pre-labeling of different protein fractions and their subsequent co-electrophoresis in a single gel. Cyanine based "CyDye DIGE Fluor minimal dyes" are used for the labeling reaction and 2D IEF/SDS PAGE is the preferential electrophoresis system for protein separation. The DIGE technology allows elimination of inconsistencies based on gel to gel variations and furthermore allows exact quantification of proteins separated by gel electrophoresis. Here we report applications of the DIGE technology in combination with another 2D gel system, Blue native/SDS PAGE. "Blue native DIGE" offers (i) systematic and quantitative comparison of protein complexes of related protein fractions, (ii) structural investigation of protein complexes, (iii) assignment of protein complexes to subcellular fractions like organelles and (iv) electrophoretic mapping of isoforms of subunits of protein complexes with respect to a larger proteome. The potential of "Blue native DIGE" is illustrated by analysis of organellar fractions from the plant Arabidopsis thaliana and the alga Polytomella. Use of the DIGE technology for topological investigations is discussed.