Haplotype analyses implied that haplotype CCTAT (MTNR1a), CTAGT (MTNR1a), and GGG (AANAT) were significantly associated with the increased risk in SLE susceptibility, but TCTAT (MTNR1a) and CTG (AANAT) appeared to be a protective haplotype (all P < 0.05). This evidence concerns the gene MTNR1A and systemic lupus erythematosus.