Objective To investigate the clinical application value of peripheral blood lymphocyte subsets expression levels in autoimmune disease(AID) among the patients with antinuclear antibody(ANA) positive .Methods 200 patients with ANA positive and 196 patients with ANA negative were selected as the experimental group and control group respectively .The experimental group adopted indirect immunofluorescence assay (IFA) and immunoblotting assay(LIA) for detecting ANA ,moreover divided into the IFA group and LIA group according to the detection results .Meanwhile the flow cytometry was adopted to detect peripheral blood T lymphocytes ,helper T lymphocytes ,cytotoxic T lymphocyte ,NK lymphocytes and B lymphocytes absolute values of each group .The detection results were statistically analyzed .Results Helper T lymphocytes ,NK lymphocytes and B lymphocytes absolute values in the experimental group were significantly lower than those in the control group ,the differences were statistically significant(P＜0 .01);in the experimental group ,helper T lymphocytes and NK lymphocytes absolute values in the IIF group were significantly lower than those in the LIA group ,the differences were statistically significant (P＜0 .01) .Conclusion Peripheral blood lymphocytes subsets can serve as the important detection indicators during the diagnosis and treatment process of AID .