Killer cell immunoglobulinlike receptor (KIR) can modulate activity of NK and T lymphocytes. To investigate if the KIR genotype possesses a susceptibility to Hashimoto′s thyroiditis (HT). MethodsThe KIR genotypes in 100 HT patients and 260 randomly selected healthy controls (the control group) were determined using PCRSSP. ResultsThe two genotype frequencies of 3DL3,2DS2,2DL3,2DP1,2DL1,2DL4,3DL1,2DS4,3DL2 and 3DL3,2DL3,2DP1,2DL1,2DL4,3DL1,3DS1,2DS1,2DS4,3DL2 were significantly higher in the patient group than those in the control group (P<0.05, P<0.01), and the genotype frequency of 3DL3,2DL3,2DP1,2DL1,2DL4,3DL1,3DS1,2DL5,2DS5,2DS1,2DS4,3DL2 was significantly lower in the patient group than in the control group (P<0.05). Genotypes possesses more than 6 inhibitory KIR genes had a lower frequency in the patient group than the control group (39% vs 56.2%, P<0.01). ConclusionDifferences of the KIR genotypes between HT patients and healthy controls may explain the pathogenesis of HT.