The Xq28 region harbors three genes that have been associated with SLE: IRAK1 and its adjacent genes TMEM187 and MECP2. To deepen our knowledge of the genetic contribution of the Xq28 region to childhood-onset SLE pathogenesis, here we genotyped 15 SNVs within this region, investigated their association with childhood-onset SLE, and examined the haplotype structure differences among various populations. Here, MECP2 is linked to systemic lupus erythematosus.