RATIONALE Stable isotope analysis is a critical tool for understanding ecological food webs; however, results can be sensitive to sample preparation methods. To limit the possibility of sample contamination, freezing is commonly used to euthanize invertebrates and preserve non‐lethal samples from vertebrates. For destructive sampling of vertebrates, more humane euthanasia methods are preferred to freezing and it is essential to evaluate how these euthanasia methods affect stable isotope results. METHODS Stable isotope ratios and elemental composition of carbon and nitrogen were used to evaluate whether the euthanasia method compromised the integrity of the sample for analysis. Specifically, the stable isotope and C:N ratios were compared for larval wood frogs ( Rana sylvatica = Lithobates sylvaticus ), an ectothermic vertebrate, that had been euthanized by freezing with four different humane euthanasia methods: CO 2 , benzocaine, MS‐222 (tricaine methanesulfonate), and 70% ethanol. RESULTS The euthanasia method was not related to the δ 13 C or δ 15 N values and the comparisons revealed no differences between freezing and any of the other treatments. However, there were slight (non‐significant) differences in the isotope ratios of benzocaine and CO 2 when each was compared with freezing. The elemental composition was altered by the euthanasia method employed. The percentage nitrogen was higher in CO 2 treatments than in freezing, and similar (non‐significant) trends were seen for ethanol treatments relative to freezing. The resulting C:N ratios were higher for benzocaine treatments than for both CO 2 and ethanol. Similar (non‐significant) trends suggested that the C:N ratios were also higher for animals euthanized by freezing than for both CO 2 and ethanol euthanasia methods. CONCLUSIONS The euthanasia method had a larger effect on elemental composition than stable isotope ratios. The percentage nitrogen and the subsequent C:N ratios were most affected by the CO 2 and ethanol euthanasia methods, whereas non‐significant trends suggested that benzocaine and CO 2 altered the stable isotope ratios. It appears that the use of MS‐222 and freezing with dry ice are the most appropriate euthanasia methods for ectothermic vertebrates. Copyright © 2013 John Wiley & Sons, Ltd.