Background: Multiple Sclerosis (MS) remains to be a public health challenge, due to its unknown biological mechanisms and clinical impacts on young people. The prevalence of this disease in Iran is reported to be 5.3 to 74.28 per 100,000-person. Because of high prevalence of this disease in Fars province, the purpose of this study was to assess the spatial pattern of MS incidence rate by modeling both the effects of spatial dependence between neighboring regions and risk factors in a Bayesian Poisson model, which can lead to the improvement of health resource allocation decisions.Method: Data from 5,468 patients diagnosed with MS were collected, according to the McDonald’s criteria. New cases of MS were reported by the MS Society of Fars province from 1991 until 2016. The effects of percentage of vitamin D intake, smoking, percentage of people with normal BMI and alcohol consumption in addition to spatial structure in a Bayesian spatio-temporal hierarchical model were used to determine the relative risk and trend of MS incidence rate in 29 counties of Fars province. Results: County-level crude incidence rates ranged from 0.22 to 11.31 cases per 100,000-person population. The highest relative risk was estimated at 1.8 in the county of Shiraz, the capital of Fars province, while the lowest relative risk was estimated at 0.11 in Zarindasht county in southern of Fars. The percentages of vitamin D3 intake and smoking were significantly associated with the incidence rate of MS. The results showed that 1% increase in Vitamin D3 intake is associated with 2% decrease in the risk of MS and 1% increase in smoking is associated with 16% increase in the risk of MS.Conclusion: Spatial analysis of MS revealed low incidence rate of this disease in the south and south east of Fars province, which is due to the effects of different covariates. As suggested by previous studies, vitamin D and smoking, among all covaiates, might be associated with high incidence of MS.