Abstract: Methods and kits for evaluating a clinical outcome of an autoimmune disease, specifically disease flare e.g. if the subject stops taking the biologic disease modifying anti-rheumatic drug (DMARD), by comparing biomarkers of CD45RA, TNF-alpha and/or CXCR5 from CD3+CD4+ T cell population are disclosed. In a specific embodiment, the ratio of first subset of CD3+CD4+CD45RA?TNFA+ (memory) T cells to a second subset comprising CD3+CD4+CD45RA+TNFA+ (naïve) T cell is determined, wherein an increase in the ratio indicates a disease flare state of juvenile idiopathic arthritis (JIA). In another embodiment, enrichment of CD45RA?CR5+ subset among the T cell population indicates likelihood of flare state in JIA via memory persistence enhancement through B cell interaction. In other embodiments, additional markers including IL-6, CCR6, CD152 and PD1 are also determined, and the enrichment of CD45RA-TNFA+IL-6+ subset among the T cell population indicates a likelihood of amplification of the autoimmune disease.