There is a current imperative to reveal more precisely the molecular pathways of early onset of systemic autoimmune diseases (SADs). The investigation of newly diagnosed drug‐naive SAD patients might contribute to identify novel disease‐specific and prognostic markers. The multiplex analysis of 30 plasma proteins in 60 newly diagnosed drug‐naive SADs, such as RA (rheumatoid arthritis, n = 31), SLE (systemic lupus erythematosus, n = 19), and SSc (systemic scleroderma, n = 10) patients, versus healthy controls (HCs, n = 40) was addressed. Thirty plasma cytokines were quantified using the Procarta Plex™ panel. The higher expression of IL‐12p40, IL‐10, IL‐13, IFN‐γ, M‐CSF, IL‐4, NTproBNP, IL‐17A, BMP‐9, PYY (3‐36), GITRL, MMP‐12, and TNFRSF6 was associated with RA; IL‐12p40, M‐CSF, IL‐4, GITRL, and NTproBNP were higher in SLE; or NTproBNP, PYY (3‐36), and MMP‐12 were increased in SSc over HCs, respectively. The cleaved peptide tyrosine tyrosine (PYY 3‐36) was elevated in RA (361.6 ± 47.7 pg/ml) vs. HCs (163.96 ± 14.5 pg/ml, mean ± SEM, ∗∗∗p = 4 × 10−5). The CI (95%) was 268.05‐455.16 pg/ml for RA vs. 135.55‐192.37 pg/ml for HCs. The elevated PYY (3‐36) level correlated significantly with the increased IL‐4 or GITRL concentration but not with the clinical scores (DAS28, CRP, ESR, RF, aMCV). We are the first to report cleaved PYY (3‐36) as a specific plasma marker of therapy‐naive RA. Additionally, the multiplex plasma protein analysis supported a disease‐specific cytokine pattern in RA, SLE, and SSc, respectively.