Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease characterized by diverse autoantibodies and varied clinical features. There is much interest in biomarkers, but diagnostic and disease activity markers in actual clinical practice remain complement, autoantibodies including anti-dsDNA antibody, leukocyte count and urinalysis. This article reviews recently studied epigenetic, protein and metabolomic biomarkers. Although there are many studies about the SLE pathogenesis and biomarkers, only some biomarkers have been validated. This is most commonly because there are few prospective longitudinal and interventional studies that validate the biomarker utility. Recently elucidated candidate biomarkers need well-designed prospective studies and standardized assays for commercialization. Moreover, continuous research for SLE pathogenesis can promote biomarker development using new technologies, such as microarrays, proteomics and metabolomics techniques.