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A quantitative analysis method of the trace elements in biological specimens using the synchrotron radiation microprobe is described. The synchrotron radiation X-ray fluorescence microprobe system is calibrated by the standard sample specially prepared for the microprobe analysis. The mass thickness of each measured point is determined by measuring Compton scattering intensity in 17–20 keV from the sample. In this way, concentration of the trace elements in samples can be measured correctly. The measured values of the biological standard reference material NBS-SRM-1577a are in good agreement with the certified values. The longitudinal concentration variations of some trace element in a single hair of pregnant women have been measured by this method