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The majority of auto-immune diseases predominate in females. Rheumatoid arthritis (RA) is one of these diseases for which female are three times more affected than men. MicroRNAs have emerged as crucial regulators of the immune system, and have been reported abnormally expressed in RA. As protein-encoding genes, miRNA-encoding genes can be affected by nucleotide single polymorphisms (SNPs) that could affect their expression levels in disease. We aimed at quantifying the expression level of miRNAs located on the X chromosome and at identifying whether differences are associated with disease and/or sex.A case–control study of 21 RA patients and 22 age- and sex-matched healthy controls was performed on peripheral blood mononuclear cells. Extraction of total RNA and DNA was performed and the expression level of 14 X-linked miRNAs quantified using real time quantitative polymerase chain reaction. Two FoxP3 polymorphisms were genotyped using the Sanger sequencing method. An analysis of expression quantitative trait loci (eQTL) was performed to detect transcriptional regulatory relationships between X-located miRNA expression levels and 2 single nucleotide polymorphisms in FOXP3 gene associated with RA susceptibility.We showed that miR-221, miR-222, miR-532, miR-106a and miR-98 expression levels were significantly different between RA and controls only when stratifying according to the sex. Furthermore, the expression level of 4 miRNAs (miR-222, miR-532, miR-98, miR-92a) was significantly different between RA female and male. We performed an eQTL analysis and showed a significant gender effect of the FoxP3 promoter polymorphism rs3761548A/C on miR-221, miR-222 and miR-532 expression levels, and of the FoxP3 polymorphism rs2232365A/G on miR-221 expression level in PBMC of RA patients.These data further support the involvement of the X chromosome in RA susceptibility. X-linked miRNAs, in the context of sex differences, might provide novel insight into new molecular mechanisms and potential therapeutic targets in RA for disease treatment and prevention.