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The synthesis and crystal structure of a mixed valent manganite CaMn3O6, equivalent to Ca2/3Mn2O4, are reported, along with the magnetic properties. The structure was determined using electron diffraction and high-resolution transmission electron microscopy and refined from X-ray and neutron powder diffraction data (a = 10.6940(3) Å, b = 11.3258(3) Å, c = 8.4881(2) Å, β = 122.358(2)°, space group P21/a, R I = 0.037, R P = 0.118). The structure is based on a framework of double chains of edge-sharing MnO6 octahedra. The corner-sharing chains form a framework with six-sided tunnels, identical to that of the CaFe2O4 structure. The Ca2+ cations are located in the tunnels. Compared to CaFe2O4, one-third of the Ca positions in the tunnels remain vacant, with an ordered distribution of vacant and occupied sites. The empty sites in neighboring Ca chains are shifted relative to each other along the c-axis by one period of the CaFe2O4 subcell, which results in a symmetry decrease from orthorhombic to monoclinic. Based on the interatomic Mn−O distances, the charge ordering in CaMn3O6 is discussed. The compound exhibits a strong anti-ferromagnetic character, and differences between the zfc and fc magnetization curves at low temperature suggest ferro- or ferrimagnetic interactions.