The present invention, in the physiological magnetic field measuring instrument, recognizes characteristic waveforms (for example, heart beats) repeatedly appearing by physiological activity from measured signal waveforms, registers one of measured heart beats as a reference waveform, evaluates the difference degree of each measured heart beat data from the reference waveform, and executes the averaging process using only waveforms whose difference degrees are less than the allowable value. The present invention registers waveforms whose difference degrees are more than the allowable value as abnormal data and puts them into the display enabled state. Discrimination information is as signed to measurement conditions necessary for measuring the physiological magnetic field and data analysis conditions and when the discrimination information is designated for measurement, the measurement conditions and analysis conditions can be read. By doing this, the physiological magnetic field measuring instrument independently selects good or defective data automatically, and a reliable automatic averaging process can be obtained, and the data processing and operation can be simplified.