Objective To explore the association between the polymorphisms of TSC1,TSC2,PTEN genes and autism in Chinese Han population.Methods 274 autism patients and 386 heahh controls were recruited,and SnaPshot technique was used to genotype the 13 tagSNPs of TSC1,TSC2 and PTEN genes.The allele,genotype and haplotype frequencies of the SNPs were compared using SHEsis and SNPStats softwares.Results Mter Bonferroni correction,the allele distribution of rs2809244 (TSC1) (x2 =9.537,P=0.002,adjusted P=0.016),rs1050700 (TSC1) (x2 =9.313,P=0.002,adjusted P=0.016),rs2072314(TSC2) (P＜0.01,adjusted P＜0.01) and rs8063461 (TSC2) (P＜0.01,adjusted P＜0.01)showed significant difference between two groups (P＜0.05).The genotype frequencies of rs2072314(TSC2)and rs8063461(TSC2) showed significant difference between two groups(P＜0.05).Moreover,the frequency of haplotype A-G (OR =14.548,95％ CI =5.450-38.830) in the haplotype block rs2809244-rs3761840 showed significant difference between two groups(P＜0.05),A-G significantly increases the risk of autism.The frequencies of haplotype A-A (OR=0.608,95％ CI =0.409-0.903,P=0.013),G-A (OR=7.812,95％ CI =5.338-11.459,P＜0.01)and G-G (OR=0.356,95％ CI =0.274-0.463,P＜0.01) in the haplotype block rs2074969-rs8063461 were identified,which were significant difference between two groups(P＜0.05),and AA and G-G significantly reduced but G-A increased the risk of autism.Conclusion The polymorphisms of TSC1 and TSC2 genes might associate with autism in Chinese Han population.