X-ray protein crystallography has been extending the target for its application. Membrane proteins and macromolecular super-complexes play important roles in biological systems, but there exist particular problems that should be overcome for their crystallographic analysis. To date appreciable number of membrane proteins and macromolecular super-complexes have been crystallized and the three-dimensional structures for some of them have been successfully determined. Here, the authors describe the problem and progress of their X-ray crystallographic analysis.