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Introduction: Alopecia areata (AA) is an autoimmune disease causing non-scarring hair loss, with both genetic and environmental factors implicated. Recent research highlights a possible role for scalp microbiota in influencing both local and systemic inflammatory responses, potentially impacting AA progression. This study examines the link among scalp microbiota imbalances, AA severity, and systemic inflammation., Methods: We conducted a cross-sectional study with 24 participants, including patients with AA of varying severities and healthy controls. Scalp microbial communities were analyzed using swab samples and ion torrent sequencing of the 16S rRNA gene across multiple hypervariable regions. We explored correlations among bacterial abundance, microbiome metabolic pathways, and circulating inflammatory markers., Results: Our findings reveal significant dysbiosis in the scalp microbiota of patients with AA compared to healthy controls. Severe AA cases had an increased presence of pro-inflammatory microbial taxa like Proteobacteria, whereas milder cases had higher levels of anti-inflammatory Actinobacteria. Notable species differences included abundant gram-negative bacteria such as Alistipes inops and Bacteroides pleibeius in severe AA, contrasted with Blautia faecis and Pyramydobacter piscolens predominantly in controls. Significantly, microbial imbalance correlated with AA severity (SALT scores) and systemic inflammatory markers, with elevated pro-inflammatory cytokines linked to more severe disease., Conclusion: These results suggest that scalp microbiota may play a role in AA-related inflammation, although it is unclear whether the shifts are a cause or consequence of hair loss. Further research is needed to clarify the causal relationship and mechanisms involved., Competing Interests: Declarations Conflict of Interest Juan Ruano is a member of the Editorial Board of Dermatology and Therapy but was not involved in the peer review or editorial decisions for this manuscript. All other (Pedro J. Gómez-Arias, Jesús Gay-Mimbrera, Irene Rivera-Ruiz, Macarena Aguilar-Luque, Miguel Juan-Cencerrado, Carmen Mochón-Jiménez, Francisco Gómez-García, Silvia Sánchez-González, Adriana Ortega-Hernández, Dulcenombre Gómez-Garre, Esmeralda Parra-Peralbo and Beatriz Isla-Tejera) co-authors declare no conflicts of interest. Ethical Approval Reviewed and approved by Provincial Research Ethics Committee of Córdoba, Spain; approval # HRP-503, August 2015. The legislation in effect in 2015 has not changed in a way that would impact the validity of the approval, and the original approved protocol remains relevant to the current study. No changes have been made to the study, such as modifications in methodology, inclusion of new participants, or alterations in study conditions, that would invalidate the initial approval. The research was conducted following the standards of good clinical practice and adhering to the principles outlined in the by the Helsinki Declaration of 1975, as revised in 1983, and Belmont Report and adhered to Spanish and European laws regarding data privacy. Before participation, all patients provided informed consent after receiving and reviewing the patient information sheet., (© 2024. The Author(s).)