The interface between a Cu(In,Ga)Se2 (CIGS) and an underlying Mo layer was studied by X-ray diffraction and high resolution transmission electron microscopy. The CIGS layer was deposited onto Mo coated soda-lime glass using the “3-stage” process. A MoSe2 layer found to form at the CIGS/Mo interface during the 2nd stage of the “3-stage” process. The thickness of the MoSe2 layer depended on the substrate temperature used for CIGS film deposition as well as the Na content of the CIGS and/or Mo layers. For higher substrate temperatures, thicker MoSe2 layers were observed. The Na in the CIGS and/or Mo layer is felt to assist in the formation of MoSe2. Current-Voltage measurements of the heterojunction formed by the CIGS/Mo interface were ohmic even at low temperature. The role of the MoSe2 layer in high efficiency CIGS solar cells is discussed.