The grain boundary character distribution (GBCD) of nanotwinned copper, fabricated by electroplating inside small-scale through-wafer vias, was characterized using a stereological interpretation of electron backscatter diffraction maps. The GBCD of electroplated nanotwinned copper, specified by five macroscopic parameters (three for the lattice misorientation and two for the grain boundary plane inclination), is similar to the GBCD of coarse-grained polycrystalline copper used here as a reference material. The GBCD was compared to calculated grain boundary energies determined from atomistic simulations. We find that the grain boundary population in the electroplated nanotwinned and coarse-grained reference copper is both on average inversely correlated to the grain boundary energies. The slopes of the relationships between grain boundary population and energy for the most highly populated misorientations (Σ3, Σ9, and Σ11) are different. The relationships are strongly influenced by the geometric constraints at the triple junctions and multiple twinning, which enhanced the observed frequencies of Σ9 boundaries. The results suggest that the grain boundary network and the GBCD in the polycrystalline specimens are strongly influenced by the microstructure, grain boundary energy, and multiple twining.