The relation between apolipoprotein (APOE) gene polymorphisms and disease progression of multiple sclerosis (MS) is controversial. The present study was designed to investigate the relation between APOE gene polymorphisms and Japanese patients with MS. We analysed the frequencies of APOE gene polymorphisms in 135 MS patients and 134 healthy controls, using PCR-RFLP. The results showed no significant differences in the distribution of APOE gene polymorphisms between MS patients and controls. With regard to disease progression, there was no association between APOE gene polymorphisms and epsilon4 allele positivity and disease progression index (EDSS/ years). Furthermore, in patients with more than 10 years of disease onset, there were no significant differences between the frequencies of epsilon4 allele and patients with EDSS of more than 6. Although the low rate of epsilon4 allele in Japan should be taken into consideration, our results showed no relation between APOE gene polymorphisms and Japanese patients with MS.