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The structural study of diluted magnetic semiconductors is important for interpreting the ferromagnetic behavior associated with the materials. In the present work, a series of low concentration Mn-doped ZnO thin films synthesized by pulsed laser deposition was studied by electron microscopy. All films show the wurtzite structure with (001) preferred growth orientation on the Si substrate. Electron diffraction experiments indicate the deterioration of the growth orientation in some areas of the films with increasing Mn concentration, and the existence of a secondary phase, of Mn2O3-type, in the films with larger Mn concentrations. High-resolution electron microscopy images confirm the existence of the secondary phase in the grain boundary of the Mn-doped ZnO phase. The magnetic properties of Mn-doped ZnO are discussed in relation to the structures of the films.