In the method and apparatus for analyzing contaminative element concentrations, a fluorescent X-ray generated by elements when an X-ray is total reflected from the surface of a substrate is detected by a fluorescent X-ray detector; a peak of the fluorescent X-ray generated by a substrate element and peaks of the fluorescent X-ray generated by other contaminative elements are separated from the detected fluorescent X-ray waveform by a peak separating circuit; and the concentrations of the detected contaminative elements are calculated on the basis of the separated peaks by a calculating circuit. In the peak detection, in particular, the peaks of the contaminative elements to be analyzed are detected from the waveform. When other peaks are present within a predetermed number of channels (energy eV) before and after each detected peak, the channel numbers and the signal intensities between the respective peaks are extracted. Further, the a true peak is determined after obtaining the evaluation values of the respective peaks, so that it is possible to separate peaks from the fluorescent X-ray waveform accurately, even if each peak is split in the observed waveform.