Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease with complex genetic inheritance. IKZF1 was established as a new susceptibility gene for SLE in a recent genome-wide association study (GWAS) in Chinese Han population. In order to examine whether expression levels of IKZF1 contribute to the pathogenesis of SLE, we estimated IKZF1 mRNA expression levels in peripheral blood mononuclear cells (PBMCs) via fluorescent quantitative reverse transcription polymerase chain reaction (RT-PCR) in 60 patients with SLE and 60 controls. We also explored whether the IKZF1 mRNA expression levels are associated with the variant of the SNP rs4917014 and the SLE Disease Activity Index (SLEDAI). The expression levels of IKZF1 mRNA in patients with SLE were significantly decreased compared with those in healthy controls (P<0.001). No significant differences were found between IKZF1 mRNA expression levels and SLEDAI scores, SNP rs4917014. Our results suggest that decreased expression of IKZF1 mRNA may be correlated with the pathogenesis of SLE.