In a method for operation of a magnetic resonance system, radio-frequency excitation pulses are radiated into a tissue that contains at least 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, to read out the signals of the at least two gradient echoes at points in time of the signal readout 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.