In a method for operation of a magnetic resonance system, radio-frequency excitation pulses are radiated into a tissue that contains at least two different tissue types, namely a first tissue type with a first resonance frequency and a second tissue type with a second resonance frequency, a readout gradient is activated with polarity changing at least twice between two radio-frequency excitation pulses; with a gradient echo of the tissue being generated by each bipolar gradient switching; the echo time thereof corresponds to the time duration from a radio-frequency excitation pulse to the gradient echo, the signals of the at least two gradient echoes are read out by activating readout gradient between two radio-frequency excitation pulses, and the points in time of the signal readout are selected such that the gradient echoes of both tissue types have the same phase position, and/or the phase position of the gradient echoes of the first tissue lies counter to the phase position of the gradient echoes of the second tissue type, or the phase positions of the gradient echoes of both tissue types relative to one another are not taken into account in the selection of the signal readout.