In this paper, we study the chord index of virtual knots, which can be thought of as an extension of the chord parity. We show how to use the chord index to enhance the quandle coloring invariants. The notion of indexed quandle is introduced, which generalizes the quandle idea. Some applications of this new invariant is discussed. We also study how to define a generalized chord index via a fixed finite biquandle. Finally, the chord index and its applications in twisted knot theory are discussed.