<p>Stunning pigs with inert gases induces less aversive behavior before loss of consciousness than stunning with high-concentration carbon dioxide (CO₂). As the amygdala is the center of emotional processing, we hypothesized to find differences in the amygdala transcriptome depending on the gas used for stunning. Therefore, 27 amygdala samples were collected from pigs that were stunned with either argon (Ar), a mixture of nitrogen (N₂) and Ar, or CO₂. From each sample, total RNA was isolated and sequenced. Compared with inert gases, CO₂ stunning induced an amygdala transcriptional profile consistent with increased fear-related processing. For example, gene set enrichment analysis identified <i>G protein‑coupled serotonin receptor activity</i> as significantly enriched only in comparisons between CO₂ stunning and inert‑gas stunning. In this context, <i>HTR1A</i> and <i>HTR2A</i>, which encode serotonin receptors, were downregulated in the animals stunned with CO₂. Both receptors have already been described to be involved in psychological disorders and fear, suggesting that CO₂ stunning induces more fear-like emotions. Together, these transcriptomic differences support previous reports of more aversive responses during CO₂ stunning. This study provides the first whole‑transcriptome analysis of porcine amygdalae following stunning with different gas mixtures and highlights candidate transcripts for benchmarking welfare outcomes of stunning gases.</p>