OBJECTIVE: To detect genetic polymorphisms associated with high serum interferon alpha (IFN-alpha) levels in juvenile dermatomyositis (JDM) and explore interactions in associated polymorphisms. STUDY DESIGN: Eighty-five children of European ancestry with definite/probable JDM were studied. Selected genetic polymorphisms that were associated with high IFN-alpha levels in 12 untreated patients with newly diagnosed JDM were genotyped in a validation cohort of 73 children with JDM and analyzed for gene-gene and gene-sex interactions. RESULTS: Untreated children with newly diagnosed JDM carrying both the osteopontin (OPN) rs28357094G and tumor necrosis factor alpha (TNF-alpha)-308 A alleles had significantly increased serum IFN-alpha levels. These 2 polymorphisms were genotyped in the validation cohort, and the OPN rs28357094G allele was more common in female subjects with JDM (odds ratio=3.97, P=.012). This OPN allele was most strongly enriched in female carriers of TNF-alpha-308A as compared with male carriers of TNF-alpha-308A (odds ratio>9.0; P=7.2x10(-3)). CONCLUSION: These data support a complex gene-gene-sex interaction between the OPN and TNF-alpha promoter regions in JDM, defining a high serum IFN-alpha subgroup within JDM. This suggests pathogenic synergy between the OPN and TNF-alpha loci in female subjects with JDM, which may underlie some of the increased incidence of this condition in girls.