We are developing a compact ultra-low-field MRI system that is composed of a SQUID gradiometer and a coil set that generates magnetic fields for capturing MR images. The magnetic interference induced from a power amplifier potentially disturbs MRI measurements. We investigated the path of the interference by experimental measurements and calculation of the magnetic field generated by the coil set. We found that the magnetic field generated from a particular gradient coil affected the SQUID gradiometer and that the level of the interference was strongly dependent on the shape of the gradient coils. When the coils' shapes are designed, minimizing the noise introduced from the power amplifier is crucial, in addition to consideration of the homogeneities of the magnetic field. © Published under licence by IOP Publishing Ltd.