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 above room temperature by doping with transition metals, especially Mnand Co.However, doping ZnO layers with these transition metals atoms may lead to the formation of various interphase precipitates, which may have magnetic properties. One of the easiest and low cost deposition method for introducing high doses of nitrogen may be deposition by rf sputtering. However, the deposited layers may be of poorer crystalline quality when doped with transition metals, and the existence of structural imperfections can impede the clarification of experimentally observed ferromagnetism in DMS materials. In this work, our aim is to develop a better understanding of the observed magnetic behaviour by carrying out a detailed microstructural analysis of Mn-doped ZnO thin films. In samples which show a ferromagnetic effect, we also observed numerous precipitates. We will report on their relationship with the deposition conditions, as well as their connection to the measured magnetic properties.