A natural calculus for describing the bound-state structure of relativistic composite systems in quantum field theory is the light-front Fock expansion which encodes the properties of a hadrons in terms of a set of frame-independent n-particle wavefunctions. Light-front quantization in the doubly-transverse light-cone gauge has a number of remarkable advantages, including explicit unitarity, a physical Fock expansion, the absence of ghost degrees of freedom, and the decoupling properties needed to prove factorization theorems in high momentum transfer inclusive and exclusive reactions. A number of applications are discussed in these lectures, including semileptonic B decays, two-photon exclusive reactions, diffractive dissociation into jets, and deeply virtual Compton scattering. The relation of the intrinsic sea to the light-front wavefunctions is discussed. Light-front quantization can also be used in the Hamiltonian form to construct an event generator for high energy physics reactions at the amplitude level. The light-cone partition function, summed over exponentially weighted light-cone energies, has simple boost properties which may be useful for studies in heavy ion collisions. I also review recent work which shows that the structure functions measured in deep inelastic lepton scattering are affected by final-state rescattering, thus modifying their connection to light-front probability distributions. In particular, the shadowingmore » of nuclear structure functions is due to destructive interference effects from leading-twist diffraction of the virtual photon, physics not included in the nuclear light-cone wavefunctions.« less