Pre-treatments are often used to remove organic “contaminant” material prior to isotopic analyses of coral skeletal samples. Here we conducted three experiments to test the pre-treatment effect of water, 30% hydrogen peroxide (H 2 O 2 ), and household bleach [5.25% sodium hypochlorite (NaClO 3 ) and 0.15% sodium hydroxide (NaOH)], on the stable isotopic composition of coral skeletal samples. First, using a mass balance approach we calculated the expected change in skeletal δ 13 C due to the removal of all organic carbon. The model showed that (1) the removal of organic carbon (which has a low δ 13 C value relative to skeletal δ 13 C) from the skeletal sample should theoretically result in a higher δ 13 C value of the remaining organic-carbon-free carbonate, and that (2) only at the highest concentrations of skeletal organic carbon within the tissue layer of corals is the contribution of the organic carbon to the overall δ 13 C skeletal value potentially large enough to be detectable by mass spectrometry. We then conducted two sets of experiments to test the model where we pre-treated a large number of skeletal samples from five species of corals with water, H 2 O 2 , bleach, or no pre-treatment for 24 h. Skeletal δ 13 C generally decreased significantly with water, bleach, and H 2 O 2 pre-treatments which is contrary to the model-predicted increase in δ 13 C following such pre-treatments. Thus, organic carbon within the skeleton is not a net source of contamination to δ 13 C analyses. Skeletal δ 18 O decreased the most with water and bleach pre-treatments. In addition, the effect of H 2 O 2 or bleach pre-treatments on either δ 13 C or δ 18 O was not consistent among species or locations. The direction of change in δ 13 C and δ 18 O with pre-treatments was no different for skeletal samples taken within or below the tissue layer. Based on our results, we suggest that pre-treatment is not necessary and recommend that pre-treatment not be performed on coral skeletal samples prior to stable isotope analysis to avoid any pre-treatment-induced variability that could significantly compromise inter-colony and inter-species comparisons.