Elemental concentrations of Sr, Fe, Zn and Cr have been measured by in-air and microbeam PIXE to track the changes during the stalagmite growth. The objective was to find the optimal parameters for the measurements of available isotope-dated stalagmite cuts from Slovenian Karst. Significant concentration fluctuations of Fe, Sr and Cr at the scale of several millimetres have been observed by in-air PIXE. Fluctuations of trace elements observed by microbeam PIXE are contributed to the sub annual periods of growth. As demonstrated, a two-dimensional Ca, Sr, Fe and secondary electron mapping is required to avoid regions with mineral inclusions and surface irregularities during line scans over the speleothems. Optimal measuring parameters for microbeam PIXE mapping of large stalagmite cuts already mapped by isotope dating are given. These measurements would account for sub-annual growth fluctuations.

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