Ternary chalcopyrite systems are of interest for a number of applications, including host materials for dilute magnetic semiconductors and thin film photovoltaic cells. There are two cation sites, 4a and 4b, in the chalcopyrites, and the location of transition-metal ions in the chalcopyrites plays an important role in determining their magnetic and electrical properties. In this work, neutron and X-ray powder diffraction of the Mn-substituted CuInSe 2 compounds, namely, CuIn 1-x Mn x Se 2 (x = 0.05 and 0.10) and Cu 1-y In 1-y Mn 2y Se 2 (2y = 0.05, 0.15, and 0.20), has been carried out. Rietveld refinements using the neutron and X-ray diffraction data reveal a site preference of manganese ions on the copper site (4a) rather than the indium site (4b), in both series, namely, under In-poor conditions and under Cu-poor and In-poor conditions. The major fraction of Mn ions occupies the copper site, which thus pushes the expelled copper ions to the indium site, resulting in antisite Cu In defects. These results can help to explain why Mn-substituted CuInSe 2 compounds display antiferromagnetic interactions instead of ferromagnetic coupling as predicted by first-principles calculations. High frequency electron paramagnetic resonance measurements suggest that the oxidation state of the manganese ions is divalent.