Moxibustion has been thought to enhance immunity in healthy condition, but suppress abnormal immune response in disease status. We collected 12 patients with systemic lupus erythematosus (SLE) and 12 healthy women who received indirect moxibustion on acupuncture points ST-36 (Zusanli) and SP-6 (Sanyinjiao) 20 minutes per day for 1 week. During the course, there were no changes of their regular medications or intercurrent infections in normal subjects and SLE patients. We found that indirect moxibustion for 1 week could elevate CD3+ and CD4+ T-lymphocytes in normal subjects, whereas decrease relative proportions of CD8+ T-lymphocytes in patients with SLE. This result confirms that indirect moxibustion has different immunomodulation in normal condition and autoimmune status. However, whether immunomodulatory effects of indirect moxibustion are beneficial for normal subjects and patients with SLE require further confirmation.