Clathrate Ba6Ge25 is prepared by melt method and spark plasma sintering. Structural transition below room temperature is studied by positron annihilation and X-ray diffraction measurements. There is a pronounced transition in the temperature range of 200-250 K which might be involved with the movement of Ba atoms in Ge cages and result in disordered structure. This transition is further confirmed by the theoretical calculation of positron annihilation states. Thus our results confirm the structural models proposed by Carrillo-Cabrera et al. (2005). The measured specific heat capacity, electric resistivity and magnetic susceptibility all show anomalous transition in the same temperature range, indicating that the movement of Ba atoms in the cage has influence on the thermal, electric as well as magnetic properties of Ba6Ge25. (C) 2015 Elsevier B.V. All rights reserved.