CaCuGe2O6 shows a strongly distorted clinopyroxene-type structure with P2(1)/c symmetry at 298 K. The Cu2+ ion at the M1 site is coordinated by six O atoms forming an octahedron, which deviates significantly from ideal geometry. Individual M1 sites are connected via common edges to form an infinite zigzag chain parallel to the crystallographic c axis. The Ca2+ ion at M2 shows a sevenfold coordination. M2 sites are connected to the M1 chain via three common edges, thereby forming a metal layer within the bc plane. Besides the strong Jahn-Teller distortion of the Cu site, the structure of the title compound differs from ;normal' clinopyroxenes by a distortion of alternate layers of Ge sites. While the Ge(A) site is fourfold coordinated by O atoms, forming infinite chains of corner-sharing chains parallel to the c axis, the Ge(B) site exhibits a fivefold coordination, thereby forming a true two-dimensional layer of edge-sharing GeO5 bipyramids. Decreasing the temperature causes a magnetic phase transition at 40 K, as monitored by a broad maximum in the magnetic susceptibility and by discontinuities in the lattice parameters. Increasing the temperature causes variations in bond lengths, edge lengths and bond angles. Most prominent is the increase of one bond length of the Ge(B) site and the increase of the tetrahedral bridging angle of the Ge(A) site. At 660 K a crystallographic phase transition is observed where the symmetry changes from P2(1)/c to C2/c. The transition is accompanied by large changes in the lattice parameters which are indicative of distinct topological changes of several structural building units. The high-temperature C2/c structure is similar to that of the germanate clinopyroxene CaMgGe2O6.