Mutated measles virus variants have been claimed as the causing agent for subacute sclerosing panencephalitis (SSPE) developing several years after the recovery from measles infection. However, immune dysfunction may be considered related to a genetic susceptibility to this rare disease. Interleukin (IL)-2 -330 (rs2069 762) and +160 (rs2069 763), IL-12 p40 3′ UTR (rs3213113), and interferon (IFN)-γ+874 (rs2430561) polymorphisms are screened by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and PCR-sequence-specific priming (SSP) methods in 87 SSPE patients and 106 healthy controls (HCs) as candidate genes of susceptibility. The distribution of the IL12B genotypes (rs3213113) showed a trend for a significant difference (P = .053). The frequency of IL12B C allele (P = .04, OR: 1.6) and CC genotype (P = .03, OR: 3.2) were both higher in SSPE patients than in HC. The IL2 -330 genotypes revealed lower frequencies of GG genotype (P = .03, OR: 0.4) as well as G allele (P = .02, OR: 0.6) in SSPE. IL2 -330+160 TG haplotype was more frequent in patients (P = .005, OR: 1.8), whereas GG haplotype was less frequent, compared to controls (P = .02, OR: 0.6). IFNG +874 polymorphism revealed no difference. These findings implicate possible effects of genetic polymorphisms in the susceptibility to SSPE, which need to be confirmed in other populations.