In this review it is shown how the physical understanding of clustering aspects allows the formulation of a unified microscopic theory of nuclear structure and nuclear reactions. In particular, the fundamental importance of the Pauli principle is stressed in resolving the contradictions between different collective and single-particle aspects of the atomic nuclei. After the general formulation of the method, which can be applied also to other many-particle systems, several illustrative examples are given for quantitative studies of bound-state scattering and reaction problems, for semiquantitative studies and for the derivation of general nuclear properties.