We report on the structural analysis of ferromagnetic Mn-doped ZnO thin films deposited by radio frequency magnetron sputtering, using transmission electron microscopy (TEM), high-resolution x-ray diffraction, and Rutherford backscattering spectroscopy (RBS) measurements. The ferromagnetic Mn-doped ZnO film showed magnetization hysteresis at 5 and 300K. A TEM analysis revealed that the Mn-doped ZnO included a high density of round-shaped cubic and elongated hexagonal MnZn oxide precipitates. The incorporation of Mn caused a large amount of structural disorder in the crystalline columnar ZnO lattice, although the wurtzite crystal structure was maintained. The observed ferromagnetism is discussed based on the structural characteristics indicated by TEM and the behavior of Mn when it is substituted into a ZnO lattice derived from RBS measurements.