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The conodont Color Alteration Index (CAI) has been widely used to determine the maximum temperature in carbonate rocks, despite recognition that conodont colour can be affected by other factors, such as diagenesis. Measurements of trace element characteristics in conodonts of varying CAI (1.5–6.0) from the Canadian Cordillera show that those specimens with the most anomalous CAI with respect to independent estimates of maximum temperature also have the highest concentrations of iron (> 3000 ppm). The adsorption of transition metals such as iron onto bioapatite crystals and permineralization by their oxides in conodont elements are herein proposed as mechanisms for the modification of CAI during diagenesis. Furthermore, the trace element characteristics of conodonts, primarily those of the lanthanide, or rare earth element (REE) series, have frequently been used as a proxy for palaeoceanographic conditions, including anoxic events. However, the impact of early diagenetic processes post-burial obscures this marine signal, and instead, the trace element characteristics of conodonts likely reflect the characteristics of pore waters or diagenetic fluids. Several geochemical ‘tools’ have been proposed to test for such overprinting of palaeoceanographic information, including Y/Ho vs. ΣREE, MREE/MREE*, U concentration, and La/Yb. However, REE and Raman structural characteristics in a suite of conodonts from the Canadian Cordillera indicate that these ‘tools’ cannot be systematically applied. The majority of conodont specimens analysed in this study appear to have been affected by post-burial diagenetic alteration using one or more of the ‘tools’, but seem to be unaltered when investigated using other ‘tools’. Additionally, several specimens which appear to be diagenetically unaltered when using the metrics of the geochemical ‘toolbox’ exhibit diagenetically induced structural changes. The geochemical ‘tools’ are thus unable to discriminate between diagenetic alteration induced before and after burial, and they should therefore be accompanied by structural analyses if REE characteristic of conodonts are used to infer palaeoceanographic conditions.