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Yttrium iron garnet has a very high Verdet constant, is transparent in the infrared and is an insulating ferrimagnet leading to its use in optical and magneto-optical applications. Its high Q-factor has been exploited to make resonators and filters in microwave devices, but it also has the lowest magnetic damping of any known material. In this article we describe the structural and magnetic properties of single crystal thin-film YIG where the temperature dependence of the magnetisation reveals a decrease in the low temperature region. In order to understand this complex material we bring a large number of structural and magnetic techniques to bear on the same samples. Through a comprehensive analysis we show that at the substrate -YIG interface, an interdiffusion zone of only 4-6 nm exists. Due to the interdiffusion of Y from the YIG and Gd from the substrate, an addition magnetic layer is formed at the interface whose properties are crucially important in samples with a thickness of YIG less than 200 nm.