Transport through nanostructures is studied at the many-body level using exact diagonalization and nonequilibrium Green's functions. Organic molecular junctions are a particular focus because of their technological promise. Work is presented regarding: (1) A π-electron model of organic molecular junctions developed using effective field theory; (2) series transmission and transmission node structure in interacting systems; (3) the effect of interactions on quantum interference and thermoelectricity in polycyclic junctions; and (4) nanoscale transport calculations using self-consistent statistical ensembles.