The combination of HLA-C1 and KIR2DL3 remained significantly associated with cerebral malaria after adjustment for the HLA-B46 and TNF alleles (OR = 2.94, 95%CI 1.47–6.58, P = 0.004) by logistic regression analysis, indicating that the combination of HLA-C1 with KIR2DL3 is an independent risk factor for cerebral malaria. Here, KIR2DL3 is linked to cerebral malaria.