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Zirconium alloys are of great importance to the nuclear industry as they have been widely used as cladding materials in light-water reactors since the 1960s. This work examines the behaviour of these alloys under He ion implantation for the purposes of developing understanding of the fundamental processes behind their response to irradiation. Characterization of zircaloy-4 samples using TEM with in situ 6 keV He irradiation up to a fluence of 2.7×1017ions·cm−2 in the temperature range of 298 to 1148 K has been performed. Ordered arrays of He bubbles were observed at 473 and 1148 K at a fluence of 1.7×1017ions·cm−2 in αZr, the hexagonal compact (HCP) and in βZr, the body centred cubic (BCC) phases, respectively. In addition, the dissolution behaviour of cubic Zr hydrides under He irradiation has been investigated.