Research and optimization of a passive low-pass filter (LPF) for a magnetic flux transformer of superconducting quantum interferometric detector (SQUID) operating in a magnetocardiographic (MCG) system, in an unshielded room, under the influence of electromagnetic interference of significant intensity have been carried out. The amplitude-frequency characteristics (AFC) of the LPF in the SQUID magnetic flux transformer are calculated for various shunt circuits, including the LPF circuit recommended by “Supracon” group for its CE2 blue model of the SQUID. The analysis of LPF circuits and their frequency response are carried out in order to ensure maximum protection of the input circuits of the SQUID from the effects of electromagnetic interference. It is shown that the optimal LPF for the MCG system is a filter with an active resistance of about 1 Ω in the shunt circuit of magnetic flux transformer. The performed calculations of the LPF intrinsic noise in the SQUID magnetic flux transformer showed that the additional noise of the shunt circuit with a 1 Ω resistor is significantly less than external noise for MCG system operating in unshielded rooms in the industrial city.