We present a theory of the microscopic origins of the surface-enhanced circular dichroism (CD) with nanostructures. Recently, nanostructures and metamaterials have been used for the enhancement of CD signals of chiral molecules. However, the complete description of microscopic origins of the surface-enhanced circular dichroism (CD) has never been achieved. We find the total CD signals of the nanostructure coupled to chiral molecules can be decomposed into two factors: the induced and inherent CD. The inherent CD comes from the molecular absorption which can be enhanced by the strongly localized optical helicity density of resonant near-fields near the nanostructure. The induced CD is originated from the asymmetric absorption of light inside the nanostructure perturbed by nearby chiral molecules upon two opposite circularly polarized light. The recent surge of interest in the surface-enhanced CD spectroscopy has been inspired by the inherent CD enhancement, but our work shows that the induced CD can significantly contribute to the total CD signal of the chiral molecule/nanostructure coupled system. Using an example of gold nanodisk arrays, we demonstrate that the inherent and induced CD can compete with each other in plasmonic nanostructures. In this presentation, we also provide design principles for CD sensor using nanostructures and metamaterials.