Background Multiple sclerosis (MS) causes significant economic burden to the patients, families, health systems and society. This study aimed to estimate the economic costs incurred by patients with multiple sclerosis at different levels of the disease.Method This was a cross-sectional study, using the Expanded Disability Status Scale (EDSS) tool for assessing the disease level of 300 (=N) patients in East Azerbaijan province, Iran. To estimate the cost of MS, a questionnaire with its validity and reliability (CVR 92% and CVI 87%) and pilot test (Cronbach's alpha score 0.89) was used. The data were collected by interviewing patients and reviewing their clinical records. Linear regression and ANOVA were used to assess the relationship between disease levels and incurred costs.Results The results revealed that the mean annual cost for patients is 97,521,740 IRR (equivalent to 2,321.94 USD) and the mean score of EDSS in patients was 3.14. The annual cost incurred by patients with mild, moderate and severe levels of disease were 83,918,150 IRR (998.05 USD), 137,772,660 IRR (3,280.30 USD) and 119,962,670 IRR (2,856.25 USD) respectively. Also, there was a significant relationship between total cost and disease severity in such a way that any increase in EDSS degree is led to 8,139,260 IRR (193.79 USD) added cost for patients.Conclusion The study results could be helpful for Iranian health managers to solve problems which are facing patients and their families.