To investigate the change of melatonin receptor mRNA expression in bilateral paravertebral muscles in AIS, congenital scoliosis (CS) and controls in order to analyze its relationship to the pathogenesis of AIS. 20 cases with average age of 15.1 ± 2.2 years and average Cobb angle of 56.2° ± 16.1° were included in AIS group. 12 cases with average age of 11.6 ± 3.2 years and average Cobb angle of 59.2° ± 33.3° were included in congenital scoliosis (CS) group. 10 cases without scoliosis comprised a control group. The mRNA expression of melatonin receptor subtype MT1 and MT2 were detected by RT-PCR method. The MT2 mRNA expression on the concave side of paravertebral muscle was higher than that on the convex side in AIS and CS groups (p<0.05), but the MT1 mRNA expression showed no significant difference. In the AIS group, the ratio of MT2 mRNA expression on the concave side compared with the convex side in cases with a Cobb angle less than 50° and cases with a Cobb angle greater than 50° showed no significant difference. The melatonin receptor expression in bilateral paravertebral muscles in AIS is asymmetric, which may be a secondary change.