In this study, we present a systematic exploration of the core/periphery structures in protein interaction networks (PINs). First, the concepts of cores and peripheries in PINs are defined. Then, computational methods are proposed to identify cores from PINs. Application of these methods to a combined yeast PIN has identified 110 k-plex cores and 138 star cores. Based on more precise structural characteristics, our studies reveal new prospects of principles and roles of proteins. Our results show that, aside from connectivity, the structural variations between different types of proteins are also related to the variation in biological properties. Two classes of 1-peripheral proteins have been identified: party peripheries, which are more likely to be part of protein complex, and connector peripheries, which are more likely connected to different complexes or individual proteins. This study may facilitate the understanding of the topological characteristics of proteins in interaction networks and thus help elucidate the organization of cellular systems.