Maya Blue, a synthetic pigment produced by the ancient Mayas in pre-Columbian America, is the combination of a fibrous clay (palygorskite) and an organic blue dye (indigo). The main features of the structure of Maya Blue are already known, although the specific interactions occurring between clay and dye have yet to be completely explained. The details of the structure were studied using the Rietveld method on neutron powder diffraction patterns collected at POLARIS (Spallation Neutron Source ISIS) on a Maya Blue sample freshly synthesized using deuterated indigo. The position of the dye molecule in the structure of Maya Blue and the nature of its interactions with the clay framework were described. In the pigment, indigo lies within the palygorskite channels partially substituting the zeolitic water previously expelled during the synthesis. The dye and the water mutually compete to occupy the clay microchannels, although some portions may be empty, containing neither indigo nor water. Furthermore, the encapsulation of indigo increases the disorder in the disposition of the residual zeolitic water. The occupancy of indigo results to be higher in the orthorhombic than in the monoclinic polymorph, presumably for the faster loss of zeolitic water in the former polymorph during heating. The quantity of indigo in the pigment is rather low (< 2 wt. %) and its molecules lie approximately on the (100) plane, moderately distorted and slightly rotated about the b axis. The stability of Maya Blue is guaranteed by strong H-bonds formed between the clay structural water and the indigo C=O group. All the present results are coherent with data obtained in previous studies.