Seizures are associated with high intracellular calcium levels. However, conditions characterized by high intracellular calcium levels, such as stroke or traumatic brain injury, do not always evoke epilepsy. We hypothesized that polymorphisms in calcium-related genes CACNA1E and Camk2d contribute to the individual variability in seizure susceptibility. The distribution of one single nucleotide polymorphism (SNP) in the CACNA1E and one in the Camk2d gene was determined in Sprague-Dawley rats that were subjected to amygdala kindling or hyperthermia-induced seizures. The pre-kindling afterdischarge threshold was significantly lower in rats with the CACNA1E GG genotype (45.2+/-6.7microA) than in the GT genotyped animals (79.3+/-53.7microA). Among hyperthermia treated rats, the Camk2d G allele was more frequent among rats that did not display behavioral seizures during hyperthermia (67%) than in animals that did show behavioral seizures during hyperthermia (52%, chi(2)(1)=3.847, p=0.05). SNPs in CACNA1E and Camk2d genes are associated with the individual variability in seizure susceptibility in two experimental seizure models.