Electro-magnetic interference (EMI) noise radiated from the DC cable of photovoltaic power conditioner systems (PCS) is a serious problem for radio transmission equipment. In order to prevent the interference, the International Special Committee on Radio Interference (CISPR) is discussing to determine a noise regulation value for this issue. To reduce the radiated noise, this paper studies the attenuation characteristics of EMI filters that are connected to both the DC- and the AC-sides of the PCS. In this paper, it is pointed out that the EMI filters do not show their own attenuation characteristic if those are connected to the PCS. In particular, when EMI filters are connected to both the DC- and AC-sides of the PCS, a specific series resonant frequency is observed and deteriorates the attenuation characteristics of both EMI filters. In order to prevent this problem, a design method for EMI filters which can reduce the common-mode EMI noise effectively, is proposed in this paper. Further, the effectiveness of the proposed method is confirmed through experiments.