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Animals used in research often have to be euthanised, especially when tissue sampling is essential. Recently, a euthanasia method, utilizing an inhalant anaesthetic 'nitrogen gas in foam' in an anoxia box (ANOXIA TM ), has gained considerable interest as it claimed to be more animal-friendly. However, it is not clear whether the use of this euthanasia method has an influence on RNA measurements. Moreover, there are no studies on the interaction effect of different euthanasia methods on the tissue sample storage conditions. The current study compared RNA measurements from two euthanasia methods (ANOXIA TM vs. T-61 ® injection) and two storage conditions (RNA later ™ vs. snap freezing) in 12 male piglets. The nitrogen anoxia method had a significantly higher RNA yield ( p < 0.01) compared to the T-61 ® method. However, no effect of the euthanasia methods on the A260/230 ratio and RIN value was observed. Tissues stored in RNA later ™ had significantly higher RIN values ( p < 0.001) compared to snap frozen samples. The present study could not find a significant difference between the two euthanasia methods in piglets, with regard to RNA quality measurements. Hence, the nitrogen anoxia technique (ANOXIA TM ) might be considered as a suitable alternative to T-61 ® for euthanasia of piglets used in research.