Serotonin regulates several aspects of brain development, and it is involved in a range of behaviors frequently disturbed in autistic disorder. The serotonin transporter is a critical component of the serotonergic system. The serotonin transporter gene (SLC6A4) is of special interest given the nature of the biological findings and the reported effects of selective serotonin reuptake inhibitors of autistic symptoms. So far the genetics researches of the SLC6A4 gene have given conflicting results. The aim of study was to investigate the association between the SLC6A4 gene and autism in the Chinese Han population. The present study was conducted with the detection of three single nucleotide polymorphisms (SNP(S)) located within the SLC6A4 gene by using the polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) analysis. We performed a family-based association study of these polymorphisms in 175 Chinese Han family trios. Linkage disequilibrium (LD) measurement (D') analysis showed the presence of LD between markers across the locus. No significant evidence of association was found at any of the markers detected by using the transmission disequilibrium test (TDT) and haplotype analyses in all samples and male samples. Our findings suggest that it is unlikely that DNA variations in the SLC6A4 gene play a significant role in the genetic predisposition to autism in the Chinese Han population or that allelic heterogeneity at the SLC6A4 loci dilutes potential disease-allele association.