We hypothesized that benign partial epilepsy in infancy (BPEI) and convulsions with gastroenteritis (CwG) may have a similar genetic background, because previous studies indicate that clinical features overlap between BPEI and CwG. As carbamazepine is effective for cessation of clustering seizures in children with BPEI and CwG, some genetic mutations regarding sodium channels may be related to the development of BPEI and/or CwG. We focused on SCN1B encoding the voltage-dependent sodium channel β subunit. We explored SCN1B mutation in 6 children with BPEI and 6 children with CwG. Genomic DNAs were extracted from peripheral blood samples accumulated from the patients and all 5 exons of SCN1B were amplified by standard PCR amplification. There were no SCN1B mutations or pathological single nucleotide polymorphisms in any of the patients, although the phenotypes of our patients were typical for BPEI or CwG. Our study demonstrated that SCN1B may not be related to the occurrence of BPEI or CwG.