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X-linked chronic granulomatous disease (X-CGD) is a rare monogenetic immunodeficiency primarily affecting phagocytes. Precipitated by mutations in the CYBB gene, patients exhibit a compromised oxidative burst, leading to recurrent infections which can be life-threatening. Curiously, autoimmune manifestations are also common in patients and carriers. Here, exploiting the cell type-specific nature of this disorder, we characterize X-CGD on a transcriptional level using single-cell sequencing. Peripheral blood from 14 X-CGD probands and 10 carriers signed onto IRB approved protocol NCT00404560, as well as from 15 controls was sampled, and PBMCs and isolated monocytes were subjected to single-cell sequencing. Probands exhibited a strong differential expression signal relative to controls. This was composed of not only genes previously described to be up-regulated in X-CGD such as IFI27, and indeed an autoimmunity-associated broader type I interferon response, but also previously undescribed genes involved in monocyte function (ARG1), antimicrobial proteins (CAMP, SLPI), and inflammasome components (AIM2). Surprisingly, expression variability was not greater in carriers relative to probands or controls, indicating a lack of cell autonomous effects from the deletion of CYBB. Interestingly, aggregate expression of differentially expressed genes in the probands was able to classify carriers from sex-matched controls with high accuracy (AUROC = 0.92), indicating the presence of an X-CGD-specific gene signature. This gene signature was also strongly co-expressed across 17 chordate species, pointing towards the disruption of ancestral pathways important in antimicrobial immunity in X-CGD probands and carriers. This work was partially supported by a Swiss National Science Foundation fellowship to S.M.