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Metamorphlings of five desert frog species were assessed for morphological abnormalities adjacent to and remote from the Nifty Copper Mine in the Great Sandy Desert of Western Australia. Abnormality rates in the most abundant species Main’s Frog (Cyclorana maini) at a remote pond were higher than that recorded in three of the four ponds adjacent to the mine. The overall abnormality rate of 2.5% therefore likely reflects the regional background levels at Nifty, which is lower than background levels at other Australian arid zone sites. Although higher rates of abnormalities were not detected in ponds adjacent to the mine, frog recruitment was inhibited in one brackish mine pond.