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Internally to your scope, the ground terminal of your leads is already connected to the safety ground of the power plug. Where that goes in your isolation transformer situation is not clear. If the scope was designed to be used only with an isolation transformer then it is possible that its ground terminal is also isolated from the power. But probably not. Before you go connecting the ground terminal anywhere, find out if that ground terminal is connected to any local ground. Just make sure that when you connect the ground lead to something in your circuit that you are instrumenting that you aren't shorting something out.Is it better to connect ground clip of oscilloscope near component i am measuring on secondary of isolation transformer or is it just as good to connect it at the voltage terminal of transformer secondary, woulnt that earth reference entire line?