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A planar electromagnetic bandgap configuration of a compact common mode filter that is laid out on printed circuit board is studied. This filter is used to mitigate the common mode noise traveling on high-speed differential signal traces. These differential signal lines may be connected to I/O connectors and cables and small amounts of common mode noise can result in significant electromagnetic emissions. The filter is obtained by a very simple planar geometry based on the electromagnetic bandgap structures. A cavity made by a rectangular/square patch (together with a solid plane underneath) has a well known and predictable resonant behavior; the coupling between the differential pair routed on top of the patterned plane and the patch cavity, occurring when the traces cross the gap between adjacent patches, is used to reduce the energy associated with the propagation of the common mode noise. The properties of this filter are studied taking into account the layout of a real differential microstrip and the number of gap crossings. A compact configuration is proposed. Time domain simulations validate the suggested layout approach.