First, an improved test apparatus for evaluating wind resistance of mechanically anchored waterproofing membrane system was furthermore developed on the basis of the previous apparatus. Then fatigue tests were carried out using it for the two kinds of mechanically anchored waterproofing systems for concrete substrate and for steel roof deck. The number of cycles to failure decreases according to increase of both vertical force and lateral force. Various defects were observed during the tests, such as rupture of membrane, large deformation of a fixing disk and enlargement of a hole in the disk for the former system, and pulling-up of a fixing screw from a disk for the latter system. It is concluded that improvement of each components elements in balance is needed to build a durable mechanically anchored systems against strong wind.