CD69 is an early T cell activation marker. In order to investigate whether the disease activity of systemic lupus erythematosus (SLE) is correlated with T cell hyperactivity as well as B cell hyperactivity, we measured the CD69 to CD3 ratio (CD69/CD3) of peripheral blood mononuclear cells (PBMCs) from 42 SLE patients and 18 healthy controls. To assess B cell activation, we measured the levels of anti-dsDNA, complement C3 and C4. Disease activity was assessed with the SLE disease activity index (SLEDAI) score. The mean value (+/- standard deviation) of CD69/CD3 for SLE patients (3.34 +/- 0.486) and healthy controls (0.92 +/- 0.015) were significantly different (P < 0.05). CD69/CD3, anti-dsDNA, C3 and C4 were all significantly correlated with SLEDAI (r = 0.50, 0.51, -0.68, -0.31, respectively, P < 0.05). CD69/CD3 could explain 25.4% of the variance in SLEDAI, and 6.7% of the variance that was independent of anti-dsDNA, C3 and C4. In patients with SLEDAI scores which were discordant with anti-dsDNA, C3 and C4 values, CD69/ CD3 still showed high correlation with SLEDAI. We conclude that CD69/CD3, which detects T cell activation is correlated with SLEDAI scores. Thus, T cell activation contributes part of the disease activity independent of B cell activity. This marker can complement in the estimation of disease activity when levels of anti-dsDNA, C3 and C4 fail to show good correlation.