In this study we fractionated polystyrene-block-polyisoprene diblock copolymers (PS-b-PI) prepared by anionic polymerization into fractions which have a narrower distribution in molecular weight as well as in chemical composition. The strategy was to use two-dimensional IIPLC: reversed phase HPLC to fractionate PI block and normal phase HPLC to fractionate PS block with a minimal effect of the other block. The working principle of the separation method was confirmed for a low molecular weight PS-b-PI (2.4 kg/mol). With the aid of matrix assisted laser desorption/ionization mass spectrometry, we found that the separation method could resolve each mer of the PS-b-PI. We extended the application to a high molecular weight diblock copolymer (24 kg/mol) and established the method as a promising tool to further fractionate block copolymers into molecular species better defined in molecular weight as well as ir composition. We observed a significant variation in average molecular weight as well as in composition of the fractionated samples. These variations were large enough to show different morphologies for the fractions taken from the same mother block copolymer.