Systemic scleroderma (SS) remains a disease with a high mortality rate; validated biomarkers for stratification and disease monitoring are still lacking. The study aimed to assess the expression of the developed panel of IFN-I-induced genes (IFI27, IFI44, IFIT3, ISG15, XAF1) in peripheral blood and affected skin of patients with SS. We tested samples of 48 SS patients and 31 healthy donors. Gene expression was analyzed using RT-qPCR (ΔΔCt) method (with normalization to the reference housekeeping gene TBP). The SFRP4 gene expression was used as a marker of skin fibrosis. Expression values of the IFN-I-induced genes were significantly (p < 0.1) increased in both blood and skin of SS patients compared to healthy donors. Comparison between compartments revealed that the expression levels of XAF1, IFI44, IFIT3, ISG15 in the patients’ blood are higher (p < 0.01), than those in skin samples. The IFI27 gene expression, in contrast, is higher in the skin (p < 0.01). The findings show that the test system developed for interferon signature assessment can potentially be used as a noninvasive tool for stratifying SS patients by analysis of RNA from peripheral blood samples, to substantiate the prescription of therapy with the IFN-I receptor blockers.