Many studies have demonstrated the role of melatonin in the etiology of AIS. Previous studies have shown that there is no evidence of mutations in the melatonin receptor 1A gene in AIS patients. In this study, we have examined the role of melatonin receptor 1B in predisposition for AIS. Using haplotype block tagging technique, a set of tagging SNPs were defined for MTNR1B from the Han Chinese data of the International HapMap project. The association between the tagging of single nucleotide polymorphisms (tSNPs) in MTNR1B region and the occurrence of AIS was studied. Method: 473 AIS girls and 311 normal controls were recruited. The age range of the patients was between 10 and 18 years old. The maximum Cobb was recorded at latest follow-up in AIS patients. Three of five tSNPs were studied; they were all located within the coding region of the MTNR1B gene. Results: There was no significant difference in the genotype or allelic frequencies (AF) of the 3 tSNPs between AIS and controls. In a case-only analysis, no difference in curve severity in AIS patients was found among patients with different genotypes (by one-way ANOVA). Discussion: The 3 tSNPs showed no association with either the occurrence of AIS or the maximum Cobb angle within AIS girls. Further analysis of the remaining tSNPs within the regulatory region of the MTNR1B gene and other related genes in the melatonin signaling pathway may provide further information on the role of the melatonin in AIS girls.