Copper indium disulfide (CuInS 2 ) is a semiconductor with a direct energy band gap of 1.53 eVan optimal value for highly efficient thin-film solar cells. But it has reached only ∼11% power conversion efficiency, far less than the theoretically achievable value of ∼30%. The cause of this low performance is not understood. A single crystal grown from 1 mol % Cu-deficient melt was studied by using atomic resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) and electron dispersive spectroscopy (EDS). While the bulk crystal is exactly stoichiometric CuInS 2 , it contains nanometer thick, structurally coherent, Cu-deficient interphases that form along rotational twin boundaries in the {112} plane. Transition zones from the bulk crystal to the interphase are observed, where In is seen to move from its normal site In In in the chalcopyrite structure to a tetrahedral interstitial site In i , while Cu remains in its normal Cu Cu position. Two In In rows of the bulk crystal merge into one row of In i , causing excess In i in the interphase. The concentrations of Cu Cu and In i reflect a ratio of Cu vacancies, V Cu , to an excess In i of ∼2. Their relative lattice positions, and the high electrical resistivity of the crystal, suggest that V Cu and excess In i "precipitate" as self-compensating, electrically neutral, [V Cu 1− In i 2+ V Cu 1− ] defect triplets. This is the first atomic-level observation of the ordered defect that has been invoked as the basic structural modifier in chalcopyrite compound homologues. The interphases introduce an optical gap of 1.47 eV. Electron trapping in band tail states, evident from a photoconductivity exponent of 0.54, is the likely cause of an unusually low electron mobility of 0.1 cm 2 V −1 s −1 . The overall result is that making CuInS 2 slightly copper-poor inserts nanometer thick layers of the interphase into the bulk crystal. This study shows that apparently conflicting results of the effect of Cu deficiency on CuInS 2 thin-film solar cells may be resolved by analyzing structure and composition at nanometer spatial resolution.