Trace element chemistry variations within individual foraminifera tests may provide valuable information on past ocean conditions. However, the combination of thin test walls and the presence of surface contaminants, not held within the carbonate structure, provide a stringent test to microanalytical methods. We analysed two tests of the benthic foraminifera Ammonia batavus by ion microprobe and compared two sets of analytical conditions. Using apertures to restrict the size of the analysed area (to ca. 10 μm diameter) reduced the effects of sample contamination. Sr concentrations were unaffected by any contamination encountered and Mg could be determined provided checks were made for silicate contamination using Al, Si and K intensities. Measured Sr concentrations (1.012–1.379 mmol mol−1) were in reasonable agreement with previously reported values. Mg concentrations (0.691–1.412 mmol mol−1) were significantly lower than values reported previously for calcitic benthic species. Significant variations in Sr concentrations occurred within individual test chambers and may reflect the juxtapositioning of calcite of different ages as the test is deposited. Significant variations in Mg and Sr concentrations also occurred between test chambers.