The T-cell immunoglobulin- and mucin-domain-containing molecules (TIMs) comprise a new family of cell surface molecules expressed on T cells. TIM-3 is expressed on T helper type 1 (Th1) cells and implicated in the pathogenesis of Th1-driven auto- and allo-immune diseases. TIM-1 is suggested to act as a co-stimulatory molecule for all T cells, but with potentially stronger effects on Th2 than Th1 cells and is associated with Th2-related immune diseases. However, the TIM molecules have not been investigated in the systemic lupus erythematosus (SLE). In this study, we examined the expression of TIM-1 and TIM-3 on peripheral blood mononuclear cells from SLE patients using quantitative real-time RT-PCR. An increased TIM-1 expression was detected in SLE patients, which correlates with interleukin-10 expression. We also found that there was a significant increase in the expression of TIM-1 in SLE patients with quite active disease (SLE disease activity index > 6), indicating that TIM-1 expression might be related to active clinical phases. In contrast, TIM-3 expression remained normal in SLE patients with low statistical power (34.89%). However, the expression of TIM-3 ligand, galectin-9 increased in SLE patients indicating an enhanced engagement of TIM-3 with its ligand in SLE, which may result in a decreased regulatory T-cell function as shown by the decreased expression of FoxP3 and TGF-beta1 in SLE. These data suggest that TIM-1 and TIM-3/TIM-3L are involved in the pathogenesis of SLE.