Transition-metal-doped ZnO is attracting the attention of researchers as a promising diluted magnetic semiconductor (DMS) material for its use in spintronics. Based on the prediction of Dietl et al., considerable effort has been focused on achieving reliable ZnO-based DMS with a Curie temperature well above room temperature by doping with transition metals, especially Mn and Co. Ferromagnetism was recently observed in insulating (Zn,Mn)O, n-type (Zn,Mn)O, and p-type (Zn,Mn)O. However, the absence of ferromagnetic ordering in (Zn,Mn)O was also reported. To develop a better understanding of the observed magnetic behavior, a detailed microstructural analysis of transition metal-doped ZnO thin films is necessary because the incorporation of transition metals may lead to structural disorder or the formation of transition metal-related micro-clusters in the films. The existence of such type of structural imperfections can impede the clarification of experimentally observed ferromagnetism in DMS materials. In this work, we have investigated samples made of a ZnO buffer layer and an Mn-doped ZnO film were deposited on sapphire at 650 C and 550 C, respectively. The as-deposited films were annealed at 850 ºC for 1 hour in air to improve the crystalline quality. The ferromagnetic Mn-doped ZnO films showed magnetization hysteresis at 5 and 300 K. This structural investigation shows that the Mn doped part of the layers contains a high density of round-shaped and elongated MnZn oxide precipitates, we report on the structural relationship between the precipitates and the ZnO matrix. Moreover, the interface between the undoped ZnO and the sapphire substrate exhibits Mn rich phase, meaning that there is a strong interdiffusion in these layers. We analyse the structure, composition and possible origin of these interfacial phases.