The accuracy of Na measurements in biological cryosections has been improved through replacement of the 8 μm Be window of the Si(Li) detector with a Super Atmospheric Thin Window (SuperATW) window mounted on a germanium electron microscope (GEM) detector. Greater accuracy of Ca measurements was also attained when a GEM detector instead of an Si(Li) detector was used for analysis of total Ca concentrations in cardiac muscle. Although the advantage of improved sensitivity for Na and Ca is lost in spot mode analysis because of the overriding contribution of biological variability, this advantage becomes important in X-ray mapping. We compared the two systems by analyzing cryosections of identical biological material under comparable conditions. We found that Si contamination in thin biological cryosections is unpredictable; it may be widespread and differ in degree in various cell compartments of the same cell. Hence, a correction for Si contamination should be included in the calculations of elemental concentrations. We suggest here a procedure for measuring and subtracting Si contamination from elemental spectra.