OBJECTIVES Th1 cells have been implicated as the causal agents in the pathogenesis of autoimmunity. SLE represents the classical prototype of systemic autoimmune disease. Copy number variations (CNVs) have been discovered to have phenotypic consequences and associate with various types of diseases. The current study aims to explore a possible association between CNVs of Th1 cell-related genes and the risk of SLE. METHODS Genomic DNA and RNA from 532 SLE patients and 576 healthy controls were extracted. CNVs of Th1 cell-related genes (T-bet, Stat4, IL-12A, IL-12B, IFN-γ, IP-10 and CXCR3) as well as Th2 and Treg cell-related genes (c-Mef, GATA3, Foxp3, IL-6 and TGF-β) were examined, and mRNA levels of IL-12B and T-bet were examined. RESULTS Frequencies of IL-12B and T-bet CNVs in SLE patients were significantly higher than those in healthy controls. CNVs of IL-12B and T-bet had no synergistic contribution to SLE. The mRNA levels of IL-12B and T-bet in the samples with more than two copies of DNA were significantly higher than those with two copies of DNA. CONCLUSIONS CNVs of IL-12B and T-bet are associated with the risk of SLE.