The living organism is a complex system consisting of numerous biological machineries that are defined as a functional unit responsible for particular biological activities, such as protein synthesis, ATP synthesis, and various kinds of metabolisms. Biological machineries may be classified into two types. The first one refers to stable assembly systems of macromolecules. This kind of machineries may sometimes be crystallized and their whole structures are determined by the X-ray crystallography. The second one does not create such a stable assembly system, but by the concerted acts of the individual macromolecules, the systems play as whole complex biological roles. The development of protein crystallography in recent years makes it possible to determine the overall three-dimensional structures of the biological machinery of both types. Three-dimensional structure determination of biological machineries would open a new era in the field of structural biology.