A common mode choke assembly includes a main core, a shunt core, and first and second two-piece bobbins. The main core has a generally rectangular main core body, and first and second core riser portions. The first and second core riser portions are connected to opposite ends of the main core body. The first core riser portion includes a first riser notch and the second core riser portion includes a second riser notch aligned with the first riser notch. The shunt core spans between and is positioned within the first and second riser notches. The first and second two-piece bobbins are positioned on opposite sides of the main core body adjacent to the first and second core riser portions. Each two-piece bobbin includes at least first and second end flanges, a passageway, and a mating surface. The assembly further includes a mounting header for receiving the main and shunt core.