In this study, the effect of chronic administration of melatonin on MRL/MpJ-Fas^lpr mice has been studied. These mice spontaneously develop an autoimmune disease that has many features resembling human systemic lupus erythematosus (SLE). In fact, histological studies showed that all female mice and most male mice exhibited glomerular abnormalities, arteritic lesions, and cellular interstitial inflammatory infiltritate ranging from mild to severe patterns. Treatment with melatonin improved the histological patterns in females and worsened it in males. Moreover, female mice treated with melatonin showed a diminution of titers of total serum IgG and IgM immunoglobulins and anti-DNAds and anti-CII autoantibodies, a decrease in pro-inflammatory cytokines (IL-2, IL-6, IFN-, TNF-, and IL-1), an increase in anti-inflammatory cytokines (IL-10), and a decrease in nitrite/nitrate. In male mice, treatment with melatonin exhibited the opposite effect worsening all the immunological parameters with an elevation of titers of autoantibodies and a prevalence of pro-inflammatory vs. anti-inflammatory cytokines. Similar results were obtained when lymphocytes from spleen and lymph nodes were cultured. Again, melatonin treatment in females decreased pro-inflammatory cytokines and increased anti-inflammatory cytokines produced by lymphocytes while in males, the effect was the opposite. These findings suggest that melatonin action in MRL/MpJ-Fas^lpr mice is sex gender-dependent probably through modulation and inhibition of sex hormones.