Despite numerous studies in many laboratories over several years, the etiology of Multiple Sclerosis (MS) is still unknown. It was suggested that some infectious agents play a role in the etiology of MS. This study included 39 patients with MS, 10 patients with other neurological disorders (OND) and a control group of 42 healthy people. There was no significant difference between MS, OND and HC groups for Chlamydophila pneumoniae based on having past infection positivity (p > 0.05). Chronic C. pneumonia infection was detected in 8 cases with MS and 3 cases in the healthy control group, and no chronic chlamydia infection was detected in patients with OND. No significant difference was found among the three groups. Antibody titres at 1/50 and higher IgG were detected in 34(87.2%), 8(80%) and 30(71.4%) of the patients with MS, OND and the healthy control group, respectively. There was no statistically significiant difference among these groups. No C. pneumoniae and HHV-6 DNA was detected in CSF samples from the patients with MS and OND. There was no significant difference for the distribution of all APO E alleles for MS and healthy control groups. Moreover, no significant difference was found in the distribution of all APO E alleles for patients who had antibody titres for past infection with C. pneumonia and HHV-6 between MS and control group. In conclusion, our data suggested that there was no contribution from the association of the C. pneumoniea and HHV-6 infections to the etiopathogenesis of the MS and our results are in concurrance with two important meta-analysis studies reported in 2006, but large scale, prospective new trials are needed to clarify this subject as proposed in meta-analysis considirations.