BACKGROUND It is known that there is a genetic predisposition to OSAHS. Polymorphisms of the 5-hydroxytryptamine (5-HT) 2A/2C receptors (5-HTR 2A/2C) genes and 5-HT transporter (5-HTT) gene may be associated with the pathogenesis of obstructive sleep apnea-hypopnea syndrome (OSAHS). OBJECTIVE In this study, we aimed to investigate the prevalence of polymorphisms of the 5-HTR 2A/2C genes and the 5-HTT gene in the Chinese Han OSAHS population. METHODS A total of 226 unrelated subjects of the Chinese Han population, including 121 OSAHS patients and 105 healthy controls, were involved in the study. The A1438G and T102C polymorphisms of the 5-HTR 2A gene, G796C polymorphisms of the 5-HTR 2C gene, and two polymorphisms (gene-linked polymorphic region [LPR] and variable number tandem repeat [VNTR]) of the 5-HTT gene were identified by polymerase chain reaction (PCR)-RFLP. RESULTS Compared with the control group, the OSAHS group had significantly higher AA genotype and A allele frequencies in the A1438G polymorphisms of the 5-HTR 2A gene, and had significantly higher frequencies of 10/10, 12/10 genotypes and the allele 10 of 5-HTT-VNTR. There were no significant differences between the genotype distribution and allele frequencies of the OSAHS group and the control group regarding the T102C polymorphisms of the 5-HTR 2A gene and the G796C polymorphisms of the 5-HTR 2C gene, the frequencies of the S or L allele and the S/S, S/L or L/L genotypes in 5-HTT-LPR. CONCLUSIONS The A1438G polymorphism of the 5-HTR 2A gene might be involved in the pathogenesis in OSAHS subjects of the Chinese Han population. Meanwhile, our findings support the argument that 5-HTT polymorphism appears to be associated with susceptibility to OSAHS, because the allele 10 of 5-HTT-VNTR might be a susceptible factor.