Fish otoliths are biogeochemical archives of environmental conditions and are a valuable tool for examining life traits. These sclerochronological life history records, accessed through geochemical analyses, are widely used in fisheries sciences, and are seeing growing use as palaeoenvironmental archives or for reconstruction of past human activities. The fidelity of such reconstructions relies on the preservation of the biogenic geochemistry, which may be altered through diagenetic processes. In this work, a methodology is provided that enables measurement of elemental concentrations with a high precision with simultaneous quality control of the data to ensure high reliability and a multi-technique sample marking strategy to ensure precise alignment. Thin sections of four archaeological and two modern otoliths from the Pacific coast of South America were examined by synchrotron mu XRF. High-definition elemental maps of sample sections up to 3.2 x 1.0 mm(2) (V x H) were produced with an on-sample spot size of 6.0 x 16 mu m(2). Thirteen elementswere detected, some of which may be useful indicators of diagenetic alteration. Strontium was accurately quantified and one sample presented local concentrations above the previously described range in literature. The quantity of collected data allows the use of statistical approaches to examine the intra- and inter-sample Sr distribution. A highly reliable profile, produced by integrating multiple points, additionally permits identification of defects and potential alteration along its length through changes in median absolute deviation. Contamination at the edge of some of the specimens was evidenced from preparation and other post-mortem alterations, even in modern samples, however diagenetic alteration in the elemental signals was not evidenced significantly further than a few hundred micrometres deep in the samples. Medium-energy SR-mu XRF therefore provides a fast and sensitive elemental probe without a visible effect on the sample, and the integration volume which limits the attainable lateral resolution in this energy range is discussed. This paper discusses the methodological limitations and opens new perspectives in the analysis of biomineral carbonate palaeoproxies. (C) 2015 Elsevier B.V. All rights reserved.