To investigate the relationship between the gene polymorphism of TLR3c.1377,TLR9-1486,and TLR9 2848 and susceptibility to multiple sclerosis(MS)in Han people of south China.A total of 123 unrelated MS patients from South China with a clinical or laboratory definition MS according to 2005 Revisions to the McDonald Criteria were studied. Another 126 controls were randomly selected from hospital staff of non-autoimmune diseases and healthy individuals. Toll like receptor (TLR) 3 and TLR 9 genotypes were determined by PCR and digested by specific restriction enzymes.There was significant difference in genotype and allele distribution of TLR3c.1377 polymorphism between the MS patients and the controls (P<0.05), and the MS patients with T allele had a lower risk (OR=0.532, P=0.014). There was no significant difference in genotypes and allele distribution of TLR9-1486 polymorphism between the MS patients and the controls. There was higher TLR9 2848 A allele frequency in the MS patients than in the controls (39.8% vs. 30.6%;P=0.037), and higher risk in MS patients with A allele than those without (OR=1.837, P=0.020). There was no significant interaction among the TLR3c.1377, TLR9-1486 and TLR9 2848 allele. Strong linkage disequilibrium was found between TLR9-1486 and TLR9 2848, but there was no significant interaction between the polymorphism of TLR9-1486 and TLR9 2848 in the MS patients.TLR3c.1377 and TLR9 2848 polymorphisms may be related to MS in Han people in south China. TLR3c.1377 and TLR9 2848 may be linked with susceptibility genes.