<p>Although recent evidence suggests that the immune system contributes to the pathogenesis of paediatric Leigh syndrome, detailed mechanistic insights are still lacking. Here, we investigated the involvement of immune system activation and inflammation in brain tissue in Leigh syndrome, using hypothesis generating methods. We compared the transcriptomes of olfactory bulb and cerebellum from male <i>Ndufs4</i>^{<i>−/−</i>} (knockout) mice (<i>n</i> = 5–6), a well-established model of paediatric Leigh syndrome. Relative to wildtype animals, knockout mice displayed enrichment of innate immune system pathways in the olfactory bulb. Unexpectedly, relative to the olfactory bulb, few pathways were enriched in the cerebellum, and none that indicated similar changes to the immune system. Innate immune system pathways in the olfactory bulb were mainly upregulated and included a large set of interferon stimulated genes, and genes involved in JAK-STAT and retinoic acid-inducible gene 1-like signalling, interleukins, interferon receptors and endogenous double strand RNA sensors. We propose that innate immune system activation starts in the olfactory bulb, is mediated by the retinoic acid-inducible gene 1-like signalling pathway in response to increased cytosolic double-strand RNA, leading to chemokines that recruit leukocytes to other brain regions to elicit an immune response. Our results fill in the gap between mitochondrial dysfunction and activation of the innate immune response, which has been reported by others. Our findings strongly suggest that immune system activation constitutes part of the Leigh syndrome pathomechanism, which is compatible with the improvement observed in mitochondrial disease patients following immune system-targeting interventions.</p> Graphical Abstract <p></p>