Objective To explore the effect of hydroxychloroquine on ultraviolet ray-induced genomic DNA hypomethylation in CD4+ T cells from patients with systemic lupus erythematosus (SLE). Methods Thirty patients with SLE and 10 normal human controls were enrolled in the study. CD4+ T cells were isolated from these subjects by using magnetic beads, and cultured. Hydroxychloroquine of 50 mg/L was added to the culture medium of CD4+ T cells before or after the exposure to narrow band ultraviolet B (NB-UVB) 311 nm.After additional culture, the levels of genomic DNA methylation in CD4+ T cells were determined with the Imprint Methylated DNA Quantification kit. Results The levels of DNA methylation was lower in SLE patients than in the normal controls [(3.922 ±2.215)% vs. (10.210 ± 5.573)%, t= 3.450, P = 0.026]. After exposure to UVB at 45 and 100 mJ/cm2, the DNA methylation level in patients with active SLE decreased from (7.235 ±3.846)% to (1.784 ± 1.033)% and (1.932 ± 1.844)% respectively (t= 3.000, 4.118, both P< 0.05). Decreased DNA methylation level was observed in CD4+ T cells from patients with active SLE compared with those from patients with stable SLE and normal human controls [(1.932 ± 1.844)% vs. (7.235 ± 3.846)% and (5.472 ±5.573)%, t = 2.648, 3.000, both P< 0.05] after irradiation with UVB of 100 mj/cm2. A significant increase in the methylation level was observed in active SLE patient-derived CD4+ T cells treated with hydroxychloroquine following the irradiation with UVB of 45 (4.698% ± 1.948%) and 100 mJ/cm2(8.698% ± 3.151%) compared with those only treated with UVB irradiation (t = 4.827, 3.184, both P< 0.05), as well as in those treated with hydroxychloroquine before and after the irradiation with UVB of 45 mJ/cm2 compared with those receiving irradiation alone [(5.404 ± 2.308)% vs. (1.784 ± 1.033)%, t = 4.827, P< 0.01]. Conclusion Hydroxychloroquine can reverse the UVB-induced genomic DNA hypomethylation in CD4+ T cells from patients with SLE,especially in those from patients with active SLE.